# block (c49b1)

The commands described in this section are used to partition a

molecular system into "blocks" and allow for the use of coefficients

that scale the interaction energies (and forces) between these blocks.

This has a number of applications, and specific commands to carry out

free energy simulations with a component analysis scheme have been

implemented. The lambda-dynamics, an alternative way of performing

free energy calculations and screening binding molecules, has also been

implemented. Subcommands related to BLOCK will be described here. To

see how to output the results of a dynamics run, please see DYNAMICS

documentation (keywords are IUNLDM, NSAVL, and LDTITLE).

Please refer to PDETAIL.DOC for detailed description of the lambda

dynamics and its implementation.

BLOCK was recently modified so that it works with the IMAGE

module of CHARMM. As some changes to the documentation were necessary

anyways, it was decided to also improve the existing documentation.

The Syntax and Function section below are relatively unchanged; the

added documentation is in the Hints section (READ IT if you are using

BLOCK for the first time!). Comments/suggestions to Stefan Boresch.

BLOCK was modified so that it works with the Ewald (simple and PME)

method of CHARMM. The Syntax and Function of BLOCK module are unchanged.

* Syntax | Syntax of the block commands

* Function | Purpose of each of the commands

* Hints | Some further explanations/hints

* Limitations | Some warnings...

molecular system into "blocks" and allow for the use of coefficients

that scale the interaction energies (and forces) between these blocks.

This has a number of applications, and specific commands to carry out

free energy simulations with a component analysis scheme have been

implemented. The lambda-dynamics, an alternative way of performing

free energy calculations and screening binding molecules, has also been

implemented. Subcommands related to BLOCK will be described here. To

see how to output the results of a dynamics run, please see DYNAMICS

documentation (keywords are IUNLDM, NSAVL, and LDTITLE).

Please refer to PDETAIL.DOC for detailed description of the lambda

dynamics and its implementation.

BLOCK was recently modified so that it works with the IMAGE

module of CHARMM. As some changes to the documentation were necessary

anyways, it was decided to also improve the existing documentation.

The Syntax and Function section below are relatively unchanged; the

added documentation is in the Hints section (READ IT if you are using

BLOCK for the first time!). Comments/suggestions to Stefan Boresch.

BLOCK was modified so that it works with the Ewald (simple and PME)

method of CHARMM. The Syntax and Function of BLOCK module are unchanged.

* Syntax | Syntax of the block commands

* Function | Purpose of each of the commands

* Hints | Some further explanations/hints

* Limitations | Some warnings...

Top

Syntax of BLOCK commands

BLOCk [int]

Subcommands:

miscellaneous-command-spec ! see

CALL int atom-selection

LAMBda real

COEFficient int int real -

[BOND real] [ANGL real] [DIHEdral real] [ELEC real] -

[VDW real] [VDWA real] [VDWR real]

NOFOrce

FORCe

FREE_energy_evaluation [OLDLambda real] [NEWLambda real] -

FIRSt int [NUNIT int] [BEGIn int] [STOP int] [SKIP int] -

[TEMPerature real] [CONTinuous int] [IHBF int] [INBF int]

[IMGF int]

INITialize

CLEAr

Energy_AVeraGe [OLDLambda real] [NEWLambda real] -

FIRSt int [NUNIT int] [BEGIn int] [STOP int] [SKIP int] -

[CONTinuous int] [IHBF int] [INBF int] [IMGF int]

COMPonent_analysis DELL real NDEL int [TEMPerature real] -

FIRSt int [NUNIT int] [BEGIn int] [STOP int] [SKIP int]

[IHBF int] [INBF int] [IMGF] int

AVERage {DISTance int int}

{STRUcture}

[PERT] [TEMPerature real] [OLDLambda real] [NEWLambda real] -

FIRSt int [NUNIT int] [BEGIn int] [STOP int] [SKIP int]

EXCLusion int int [int int] [int int]

ADEXclusion int int

LDINitialize int real real real real [real]

RMBOnd RMANgle

LDMAtrix

LDBI int

LDBV int int int int real real int

THBV COLL [int|ALL] real real

THBV INDE [int|ALL] [real|AUTO]

LDRStart

LDWRite IUNL int NSAVL int

RMLAmbda {internal_energy_spec}

internal_energy_spec ::== BOND 12BOnd 13BOnd THETa|ANGLe PHI|DIHEd IMPHi|IMPR CMAP

SAVE

UNSAve

QLDM [THETa]

QLMC [MCTEmperature real] [FREQ int] [MCSTep int] [MAX real]

MCIN int {real .... real}

MCDI real

MCRS

MCLEar

MSLD [int_1 int_2 ... int_nblocks | NSITe int] { FNEXponential [real] }

{ FNXS [real_1 ... real_nsites] }

{ FNSIn }

{ F2Exponential }

{ F2Sin }

{ FFIX }

! note: int_1 must be 0, block 1 = environment = Site 0

BLASsign int_block int_site

MSMAtrix

LANG [TEMP real]

RSTP int real

" Dual-topology Softcore"

[PSSP] ! use soft core potentials for interactions in between

! blocks. This option is remembered. With

! the PSSP keyword, two parameters, ALAM and DLAM can

! be set.

[ALAM real] ! Separation parameter for elec. interaction (defaults to 5A^2)

[DLAM real] ! Separation parameter for LJ interaction (defaults to 5A^2)

[NOPSsp] ! Turn off use of soft core interactions.

NB! This requires FAST OFF and nonbond options SHIFT VSWITCH.

" -- H. Li and W. Yang

MCFRee EXFReq int FINI real FFIN real FLAT real

MCLAmd int LAMD0 real LAMD1 real ....... LAMD[int-1] real

HYBH real ! HYBrid Hamiltonan module (HYBH).

OUTH int ! HYBH

TSTH real [<update-spec>] ! HYBH

PRIN ! HYBH

PRDH ! HYBH

CLHH ! HYBH

SOFT [W14 | ON | OFF]

SOMM "CHARMM/OpenMM implementation of softcore"

PMEL [NN | EX | ON | OFF]

FLAM string int

SCAT [ON | K [real] | OFF]

CATS atom-selection

NSOB int [RALF real] [LEXP real] [BLEX real]

SOBO int atom-selection1 atom-selection2

RLFR [ON | OFF]

END

Syntax of BLOCK commands

BLOCk [int]

Subcommands:

miscellaneous-command-spec ! see

**»**miscomCALL int atom-selection

LAMBda real

COEFficient int int real -

[BOND real] [ANGL real] [DIHEdral real] [ELEC real] -

[VDW real] [VDWA real] [VDWR real]

NOFOrce

FORCe

FREE_energy_evaluation [OLDLambda real] [NEWLambda real] -

FIRSt int [NUNIT int] [BEGIn int] [STOP int] [SKIP int] -

[TEMPerature real] [CONTinuous int] [IHBF int] [INBF int]

[IMGF int]

INITialize

CLEAr

Energy_AVeraGe [OLDLambda real] [NEWLambda real] -

FIRSt int [NUNIT int] [BEGIn int] [STOP int] [SKIP int] -

[CONTinuous int] [IHBF int] [INBF int] [IMGF int]

COMPonent_analysis DELL real NDEL int [TEMPerature real] -

FIRSt int [NUNIT int] [BEGIn int] [STOP int] [SKIP int]

[IHBF int] [INBF int] [IMGF] int

AVERage {DISTance int int}

{STRUcture}

[PERT] [TEMPerature real] [OLDLambda real] [NEWLambda real] -

FIRSt int [NUNIT int] [BEGIn int] [STOP int] [SKIP int]

EXCLusion int int [int int] [int int]

ADEXclusion int int

LDINitialize int real real real real [real]

RMBOnd RMANgle

LDMAtrix

LDBI int

LDBV int int int int real real int

THBV COLL [int|ALL] real real

THBV INDE [int|ALL] [real|AUTO]

LDRStart

LDWRite IUNL int NSAVL int

RMLAmbda {internal_energy_spec}

internal_energy_spec ::== BOND 12BOnd 13BOnd THETa|ANGLe PHI|DIHEd IMPHi|IMPR CMAP

SAVE

UNSAve

QLDM [THETa]

QLMC [MCTEmperature real] [FREQ int] [MCSTep int] [MAX real]

MCIN int {real .... real}

MCDI real

MCRS

MCLEar

MSLD [int_1 int_2 ... int_nblocks | NSITe int] { FNEXponential [real] }

{ FNXS [real_1 ... real_nsites] }

{ FNSIn }

{ F2Exponential }

{ F2Sin }

{ FFIX }

! note: int_1 must be 0, block 1 = environment = Site 0

BLASsign int_block int_site

MSMAtrix

LANG [TEMP real]

RSTP int real

" Dual-topology Softcore"

[PSSP] ! use soft core potentials for interactions in between

! blocks. This option is remembered. With

! the PSSP keyword, two parameters, ALAM and DLAM can

! be set.

[ALAM real] ! Separation parameter for elec. interaction (defaults to 5A^2)

[DLAM real] ! Separation parameter for LJ interaction (defaults to 5A^2)

[NOPSsp] ! Turn off use of soft core interactions.

NB! This requires FAST OFF and nonbond options SHIFT VSWITCH.

" -- H. Li and W. Yang

MCFRee EXFReq int FINI real FFIN real FLAT real

MCLAmd int LAMD0 real LAMD1 real ....... LAMD[int-1] real

HYBH real ! HYBrid Hamiltonan module (HYBH).

OUTH int ! HYBH

TSTH real [<update-spec>] ! HYBH

PRIN ! HYBH

PRDH ! HYBH

CLHH ! HYBH

SOFT [W14 | ON | OFF]

SOMM "CHARMM/OpenMM implementation of softcore"

PMEL [NN | EX | ON | OFF]

FLAM string int

SCAT [ON | K [real] | OFF]

CATS atom-selection

NSOB int [RALF real] [LEXP real] [BLEX real]

SOBO int atom-selection1 atom-selection2

RLFR [ON | OFF]

END

Top

1) BLOCk [int] enters the block facility. The optional integer is

only read when the block structure is initialized (usually the first

call to block of a run) to specify the number of blocks for space

allocation. If not specified, the default of three is assumed.

2) END exits the block facility. The assignment of blocks, the

coefficient weighting of the energy function, the force/noforce

option, etc. remain in place. For the terms of the energy function

that are supported, each call to ENERGY (either directly or through

MINIMIZE, DYNAMICS, etc. commands) results in an energy and force

weighted as specified. The matrix of interaction coefficients is

printed upon exiting.

3) CALL removes the atoms specified by "atom-selection" from their

current block and assigns them to the block number specified by the

integer. Initially all atoms are assigned to block 1. If atoms are

removed from any block other than block 1, a warning message is

issued. If blocks are assigned such that some energy terms (theta,

phi, or imphi) are interactions between more than two blocks, a

warning is issued when the END command is encountered. (Take such

warnings seriously; this is a severe error and indicates that

something is wrong. However, the problem might be not the CALL

statement (or the atom selection) itself; quite possibly your hybrid

molecule was generated improperly)

4) LAMBda sets the value of lambda to "real". This command is only

valid when there are three blocks active. Otherwise multiple COEF

commands may be used to set the interaction coefficients manually.

LAMBda x

is equivalent to (let y=1.0-x)

COEF 1 1 1.0

COEF 1 2 y

COEF 1 3 x

COEF 2 2 y

COEF 2 3 0.0

COEF 3 3 x

5) COEF sets the interaction coefficient between two blocks (represented

by the integers) to a value (the real number). When the block facility

is invoked, all of the atoms are initially assigned to block 1 and all

interaction coefficients are set to one. The required real value

(first specified) scales all energy terms expect those specific terms

which are named with alternative corresponding scale factors.

The name "VDWA" and "VDWR" correspond to the Attractive and Repulsive

terms in the Lennard-Jones potential respectively. That is they allow

one to independently scale the attractive (r^(6)) and repulsive terms (r^(12))

independently.

6) NOFOrce specifies that in subsequent energy calculations, the

forces are not required. This is economical when using the

post-processing commands (FREE,EAVG,COMP). Forces may be turned back

on with the FORCe command; this is necessary before running

minimizations and dynamics if there was a prior NOFO command.

7) FREE calculates a free energy change using simple exponential

averaging, i.e. the "exponential formula". If the old and new lambdas

(OLDL,NEWL) are specified (can only be done when three blocks are

active), the perturbation energy is calculated for these values (i.e.

FREE gives you the free energy difference between NEWLambda and

OLDLambda via perturbation from the lambda value at which your

trajectory was calculated. If not, the current coefficient matrix is

used (FREE should be used with three blocks, and the use of OLDL and

NEWL is recommended). FIRSt_unit, NUNIt, BEGIn, STOP, and SKIP

specify the trajectory/ies that is/are to be read (for a further

description see the TRAJ command elsewhere in the CHARMM

documentation). TEMPerature defaults to 300 K and gives the

temperature value to be used in k_B*T. CONTinuous specifies the

interval for writing cumulative free energies. A negative value

causes binned (rather than cumulative average) values to be written.

Be careful to make sure that you use correct non-bonded lists (see the

hints section!)

8) INITialize is called automatically when the BLOCK facility is

first entered and may also be called manually at some other point.

All atoms are assigned to block one and all interaction coefficients

are set to their initial value.

9) CLEAr removes all traces of the use of the BLOCK facility. The

next command should generally be END, and then CHARMM will operate

as if BLOCK had not ever been called.

10) EAVG The average value of the potential energy during a simulation

can be calculated with the EAVG (Energy_AVeraGe) command. The parsing

is very much like the FREE command above. The most frequent use of

this command is to calculate the average value of dV/dlambda during

the course of a simulation for use in thermodynamic integration.

CONTinuous specifies the interval for writing cumulative free

energies. A negative value causes binned (rather than cumulative

average) values to be written. Be careful to make sure that you use

correct non-bonded lists (see the hints section!) The command accepts

the OLDL / NEWL option, similarly to FREE, but for EAVG it is

recommended to set up the interaction matrix (using COEF commands)

yourself -- see the hints section.

11) [COMP] The COMP module is essentially a modified version of the

EAVG module which aside from calculating <dU/dl> = <U_1 - U_0> at a

given value of lambda l(i) will also give you expectation values of

this quantity at l(i+-1), l(i+-2) etc. based on perturbation theory.

COMP requires 4 blocks. Put the usual WT (reactant) in block 2 and

MUT (product) in block 3. Put the portion of the environment whose

contribution to the free energy change is desired into block 4 (this

can be everything else, or just a subset) (Note that the same can be

achieved easily with the EAVG command) You have to set up your own

coefficient matrix. Much of the parsing is like the EAVG command.

CONT is not supported. Two special subcommands (required) are DELL

and NDEL. The normal output of COMP is <U_1 - U_0> evaluated at the

lambda of the simulation. However, COMP also evaluates the same

ensemble averages perturbed to lambda = lambda +/-

{0,1,2,...NDEL}*DELL. This (sometimes) helps the quadrature in

thermodynamic integration. Note that NDEL must be at least 1, and

DELL should not be zero. (You have to specify these values; the

default values will lead to an invalid input, i.e. you bomb...) Be

careful to make sure that you use correct non-bonded lists (see the

hints section!) A word of warning: If your initial ensemble average

(at the lambda of the simulation) is not well converged, then your

perturbed values are most likely random numbers. The approach taken

by COMP is theoretically sound, but it should only be applied if

convergence has been established! The output format of COMP is

somewhat messy: COMP first prints <dU/dl> = <U_1 - U_0> at lambda =

lambda - NDEL*DELL

lambda - (NDEL-1)*DELL

...

lambda

lambda + DELL

...

lambda + NDEL*DELL;

then it prints an average (integral) value over these results. The

meaning of this last value is unclear to me. In earlier versions of

this documentation, COMP has been recommended over EAVG. In my

experience the opposite is true. There is little COMP can do which

you can't do with EAVG (aside from obtaining expectation values for

dU/dl). (Maybe the unclear output of the COMP module is the main

reason why I don't like it).

12) [AVER] The AVERage command is used to extract ensemble average

structural properties from a dynamics simulation. Features in this

implementation allow averages taken over ensembles that are perturbed

from that which the simulation corresponds to. This is particularly

useful for calculating the average structure expected at lambda=0.0

from a simulation run at lambda=0.1, for example. One may calculate

average structures [STRUcture] and average distances [DISTance int

int; where the two integers are the atom numbers between which the

average distance is requested], currently. The PERT keyword indicates

that a perturbed ensemble from the dynamics trajectory is desired,

with TEMPerature giving the temperature to use in the exponential for

the perturbation (defaults to 300 K), OLDLambda and NEWLambda are the

lambdas for which the simulation was run and for which the ensemble is

requested, respectively (only valid if three blocks are active; if

these are not specified, the perturbation energy is calculated with

the current coefficient matrix), and the remaining keywords are used

to specify the trajectory. NOTE: TO THE BEST OF MY KNOWLEDGE THIS

COMMAND HAS NOT BE MAINTAINED (so you are on your own if you use it!)

12a) [EXCL] The EXCLusion command allows you to create exclusions between

and within blocks, and thus eliminates the need to add them to the

residue/patch definitions in the rtf. For example, one can exclude

the non-bonded interactions between block i and blok j, as defined

by the block selections from call i {selection} and call j {selection},

with the block subcommand:

EXCL i j

where i and j are the integers corresponding to the blocks i and j,

respectively. This is, in principle, a powerful way to set up

interesting non-bonded exclusions, but was designed primarily for use

with multi-site lambda dynamics to eliminate the need to add the

long list of multiple-site exclusions to the rtf residue and patch residue

definitions. For examples of the use of this command, see:

c41test/blockexcl_test.inp and c41test/msld_test2.inp.

[ADEX] The ADEXclusion command adds to the list of exclusions created

with the EXCLusion command. (EXCLusion overwrites previous exclusions

when called a second time.) This enables the automated setup of

exclusions in a loop, when the number of exclusions is too large to

fit on a single charmm script input line.

13) LDINitialize specifies input parameters for running lambda

dynamics. It sets up the value of lambda**2, the velocity of

the lambda, its mass and reference free energy (or biasing potential).

E.g, the following input lines set up

parameters for the third lambda with [lambda(3)]**2 = 0.4,

lambdaV(3) = 0.0, lambdaM(3) = 20.0, and lambdaF(3)=5.0 (note that lambdaF(1)

should always be set to zero).

LDIN 3 0.4 0.0 20.0 5.0

For more details, see Node Hints, section "lambda-dynamics simulations".

14) LDMAtrix will automatically map the input lambda**2 values onto the

coefficient matrix of the interaction energies (and forces) between

blocks.

15) LDBI provides an option on applying biasing potentials on lambda

variables. The integer value specifies the total number of biasing

potentials to be used. E.g,

LDBI 3

will include total of 3 biasing potentials in the simulation.

16) LDBV sets up the specific form of the biasing potentials. At the

moment, the functional form is of power law and allows three different

classes (for details see "the actual simulations"). The input format is

LDBV INDEX I J CLASS REF CFORCE NPOWER

e.g.

LDBV 2 2 3 3 0.0 50.0 4

will assign the second biasing potential acting between lambda(2) and

lambda(3). The potential form belongs to the third class with reference

value of zero, the force constant of 50 kcal/mol and the power of four.

*) THBV uses theta biasing during MSLD theta dynamics to reduce the

amount of time spent sampling alchemical intermediates which allows

simulations with increased numbers of substituents. Two theta biases

are available, a collective bias (COLL)

nhigh(s) = sum((0.5*sin(theta(s,i))+0.5)**POWER,i)

nlow(s) = sum((-0.5*sin(theta(s,i))+0.5)**POWER,i)

V = 0.5*COEF*((nhigh(s)-1)**2+(nlow(s)-nsub(s)+1)**2)

where s and i are site and substituent indices, respectively; and an

independent bias (INDE)

V = sum(-b(-0.5*sin(theta(s,i))+0.5)^4,i)

with a default b coefficient of b=B*kT

B = 0.5*ln(0.125*pi*Ns^2*B)

The second argument of THBV chooses the collective bias or the independent

bias. The third argument specifies a site, by number, or if the keyword ALL

is used, will apply the bias to all sites. For the collecitve bias the

syntax

THBV COLL ALL COEF POWER

will set the coefficient to COEF, (kT is recommended), and will set the

power to POWER (2 is recommended).

For the independent bias, the syntax

THBV INDE ALL AUTO

will set the b value to the defalt value indicated above, and

THBV INDE ALL COEF

will set the coefficient to the real value given by COEF.

17) LDRStart is used to restart the lambda dynamics runs.

18) LDWRite specifies the FORTRAN output unit No. and the frequency

for writing lambda histogram by assigning an integer to IUNL and an

integer to NSAVL. (IUNL and NSAVL can be reset in DYNAmic command,

see

19) RMBOnd and RMANgle are used when no scaling of bond and angle energy

terms is desired.

20) RMLA is used when no scaling of bond, angle, proper torsion, and

improper torsion terms are desired. This option always works with block module.

The keywords: "RMBOnd" and "RMANgle" work only in lambda-dynamics.

COEF command can work in the same way when lambda-dynamics or hybrid-MC/MD are

not used.

e.g.

"RMLA BOND" = "COEF real BOND 1.0"

RMLA BOND removes scaling for both normal bond and Urey Bradley bond terms.

Use RMLA 12BOnd to remove bond scaling only and 13BOnd to remove Urey

Bradley scaling only.

21) SAVE saves the decomposed-energy file for post processing in the TSM

module. This command gives a choice for free energy calculation with

block module to get free energy without saving the trajectory file.

The condition and the name for the decomposed-energy file can be defined

in the dynamics module. (» dynamic keyword: IBLC, NBLC)

22) UNSAve removes the traces of the use of SAVE command shown above.

23) QLDM turns on lambda-dynamics option. LDIN command also turns on

the lambda-dynamics option only when QLMC turns off.

24) QLMC turns on hybrid-MC/MD option. If QLMC option is on, LDIN commands

do not activate the QLDM option.

In this version, we do not re-assign the velocity of the atoms when

chemical variables (lambda) are changed by MC method. Therefore, the kinetic

terms suddenly change into the different phase space. The stochastic dynamics

may diminish such artificial effects and help to reach the canonical ensemble.

QLMC and QLDM are exclusive and latest choice is active.

QLMC command should specify conditions for hybrid-MC/MD.

e.g.

QLMC MCTEmperature 300.0 FREQ 10 MCST 5 MAX 0.9

IN the above example, the temperature used for sampling the chemical space

by MC method is 300.0 [Kelvin]; MC sampling works every 10 molecular dynamics

steps (using for sampling of the atomic space); in one MC sampling, 5 trials

are examined; the scale factor (lambda^2) for the selected ligand is assigned

to 0.9 and the rest of ligands (L-1) have the scale factor 0.1/(L-1).

Different temperature can be defined in the lambda-dynamics and hybrid MC-MD

for atomic variables and chemical variables.

25) MCIN allows the intermediate states in which only two ligands have non-zero

lambda values in hybrid-MC/MD method.

e.g. (Three ligands system)

MCIN 5 0.0 0.25 0.5 0.75 1.0

5 means that each ligand may have one these five scalings:

0.0, 0.25, 0.5, 0.75, and 1.0.

In this condition, CHARMM recognizes the following chemical states:

(SCALE FACTOR)

STATE NO. LIG_A LIG_B LIG_C

1 1.0 0.0 0.0

2 0.0 1.0 0.0

3 0.0 0.0 1.0

4 0.25 0.75 0.0

5 0.75 0.25 0.0

6 0.25 0.0 0.75

7 0.75 0.0 0.25

8 0.0 0.25 0.75

9 0.0 0.75 0.25

10 0.5 0.5 0.0

11 0.5 0.0 0.5

12 0.0 0.5 0.5

26) MCDI (increment) specifies the step size to move in lambda chemical

movement. It allows intermediate states in which more than two ligands

can have non-zero lambda values in hybrid-MC/MD method. "MCDI" requires the

uniform interval for the definitions of the intermediate states.

Step size must satisfy:

Stepsize = 1.0/integer.

Example: Three ligands system

MCDI 0.25 ! 0.25 shows the step size to move in lambda chemical movement.

In this condition, CHARMM recognizes next chemical states.

(SCLE FACTOR)

STATE NO. LIG_A LIG_B LIG_C

1 1.0 0.0 0.0

2 0.0 1.0 0.0

3 0.0 0.0 1.0

4 0.25 0.75 0.0

5 0.75 0.25 0.0

6 0.25 0.0 0.75

7 0.75 0.0 0.25

8 0.0 0.25 0.75

9 0.0 0.75 0.25

10 0.5 0.5 0.0

11 0.5 0.0 0.5

12 0.0 0.5 0.5

13* 0.25 0.25 0.5

14* 0.25 0.5 0.25

15* 0.5 0.25 0.25

It is possible for MCDI to produce a state in which three ligands take

non-zero lambda values as shown with the asterisk (states 13, 14 and 15).

"MCDI" seems to be more general, but "MCIN" allows non-uniform

intervals. Thus, small step sizes can be assigned near end points.

27) MCRS ignores the force for lambda coming from the restraining potential

in lambda-dynamics. It also ignores the restraining potential energy when

chemical space is sampled by MC method. CMC/MD (Chemical Monte Carlo &

molecular dynamics) method can be carried out by combining this command

with QLMC.

28) MCLEar removes the traces of the use of QLMC command shown above.

BLOCK CLEAr command also removes the all traces of the use of QLMC.

MCLEar removes the traces of QLMC, while BLOCK CLEar removes all traces of the

BLOCK module.

29) LANG turns on the interaction between lambda variable and langevin

heatbath. In general, weak interaction between lambda variables and atoms

produced large deviations from the target temperature. Different temperatures

for lambda and atoms make nonequilibrium states and gave incorrect free

energies. Therefore, we recommend that LANG turn on in any lambda-dynamics

simulations. LEAP FROG integration method is required when using the LANG

option.

30) RSTP adds the restraining potential for the unbound states ligands

in lambda-dynamics and hybrid-MC/MD method to keep the physical low energy

states. The type of the restraining potential used with RSTP is;

R = alpha *(1 - lambda^2)* ( V - F )

i i i i

It disappears when this ligands is in bound state (lambda=1).

e.g.

REST 3 0.3

3 means the type of the restraining potential; 0.3 shows the alpha value.

There are three types for the restraining potential.

Type 1 Both environmental atoms and the ligands feel the restraining potential.

Umbrella sampling technique is used to remove the bias effect coming

from the restraining potential.

Type 2 The fixed average structure of the environmental atoms are assigned into

Block 2. The restraining potential was calculated Ri is defined as a

function of the fixed environmental atoms and the ligands.

When the system is flexible and the difference between the real

coordinates of the environmental atoms and fixed average coordinates

are considerably large, the convergence tends to slow.

Type 3 When the environmental atoms form the specific structure and vibrated

around the minimum, the fixed average structure of the environmental

atoms are similar to those of the real time coordinates.

Therefore, the force coming from the restraining potential can be

approximated zero as an average. If such a condition is satisfied,

the environmental atoms can be ignored the force coming from the

restraining potential and the ligands only feel the restraining

potential.This approximation may have a problem when we handle the

unstructured system like gas or liquid.

The utility program, post_ldm_mcmd.exe is prepared for calculating the free

energy differenes both without or with the restraining potential in

lambda-dynamics or hybrid-MC/MD method.

This program is saved in "support/post_analysis".

31) MCFRee EXFReq int FINI real FFIN real FLAT real is the main subcommand for

the definition of simulated scaling simulations. Here, EXFReq int is to set up

the frequency for Monte Carlo acceptance and rejection of the lambda space

move. FINI real is to set up the initial modification factor, usually as

2.71828 following the original Wang-Landau algorithm. FFIN real is to set up

the cutoff value for the final modification factor. FLAT real is to set up

the cutoff value for each cycle of flatness judgment.

Reference: Li, H., Fajer, M., and Yang, W. 2007. Simulated scaling method for

efficient localized conformational sampling and simultaneous alchemical free

energy simulation: A general method for MM, QM, and QM/MM simulations.

J. Chem. Phys. 126:024106.

32) MCLAmd int LAMD0 real LAMD1 real ...... LAMD[int-1] real is an additional

facility for the flexible usage of the simulated scaling method. Here, [int]

is to define the number of lambda values. LAMD0 is the first lambda value,

LAMD1 is the second one, ...., LAMD[int-1] is the last one.

33) HYBH , HYBrid_Hamiltonian module. Implementation of the truncation

scheme described in "Ensemble Variance in Free Energy Calculations by

Thermodynamic Integration: Theory, Optimal "Alchemical" Path, and

Practical Solutions", A.Blondel (2004) J.Comp.Chem 25, 985-993.

Details on the method should be sought therein. In brief, the

implementation is based on dual topology (although single topology

could be used under some conditions), the bonded terms (bond, angle

and Urey-Bradly) are kept unchanged, dihedral and impropers are

modified according to simple quadratic scheme (w_product=(3.l+1).l/4),

and electrostatic and van der Waals are treated together with a

truncation scheme reminiscent of soft-core vdw to minimize the

numerical fluctuations of the integrant (hence Optimal "Alchemical"

Path). Ewald sums and correction terms associated appeared soft

enough to be treated according to linear scaling of the charges,

allowing direct analytical calculation of dEwald/dl. A benefit of the

method, in addition to the fact that the integrant has limited

numerical fluctuations, is that it also produce a linear evolution of

the integrant along lambda (or l) in regular cases.

The implementation attempts to supports most of non-bonds, image

and Ewald sums options and warnings are made. Slow routines are not

currently supported. However, it is advised to test the results when

new combination of options are used. CMAP is not currently supported.

Associated commands are called from within the BLOCk module and are:

HBYH real: Switchs the module on and sets the lambda parameter.

Due to the theoretical properties of the method, evenly spaced

values should be sufficient (eg. l=(2i-1)/20). The product part

(bloc 3) is weighted according to l as explained above, and the

reactant part (bloc 2) is weighted according to (1-l) as explained

above.

OUTH int: Sets the output unit for the dE/dl terms.

TSTH real [<update-spec>]: Sets dl and tests the derivatives (dE/dl)

by finite differences (E(l+dl)-E(l-dl))/2/dl. None zero components

of the energy are printed.

PRIN : Prints dE/dl with the usual ENERGY printing format.

PRDH : Writes dE/dlambda components to outh unit. Replaces the

automatic writting performed during dynamics, for example, when

re-reading a trajectory for post-processing.

The current form of the output is formatted, two line per dynamic step.

R l dDIHEr dIMDIHEr dVDWr dELECr dEWKSUMr dEWSELFr d(EWEXCL+EWQCOR+EWUTIL)r

P l dDIHEp dIMDIHEp dVDWp dELECp dEWKSUMp dEWSELFp d(EWEXCL+EWQCOR+EWUTIL)p

Format: (a1,1x,f6.4,7(1x,1pg24.16e2))

CLHH: Clears the data structure for truncation scheme and switchs off

the module without changing the rest of the block setup. Note, the

BLOCk/CLEAr command also switchs off the module.

No analysis routine is currently supplied as careful convergence

analysis should be undertaken. It is advised that additions of the

terms be made at least in real*8 format as truncation errors might

be significant otherwise.

Testcases c35test/block_hybh.inp & block_hybh_ew.inp are provided.

34) MSLD invokes Multi-Site lambda-dynamics. The integers which follow

the keyword indicate the "Site" to which atoms within each block are

assigned. The first block must be assigned to Site 0 (the "environment"

atoms). Currently, QLDM THETA must be specified prior to invoking MSLD.

If there are too many blocks to assign each to a site in the MSLD

command, (due to CHARMM variable and line length limitations),

MSLD may be invoked with the NSITe option, e.g. "MSLD NSITe int",

where int specifies the number of sites, and blocks may be assigned

to sites individually later in the block section using

"BLASsign int_block int_site", which assigns block int_block to site

int_site.

Several different functional forms of lambda have been implemented. The

default functional form is FNEX 5.5. (Note: these functions are for

lambdas associated with all blocks except for block 1--ie. the environment

atoms at site 0.)

i) n-block normalized exponential: FNEX [c]

Note: Use FNXS [c1 c2 ... cnsites] to set a different c for each site

num(Site_a,sub_i) = exp(c*sin(theta(Site_a,sub_i))

lam(Site_a,sub_i) = num(Site_a,sub_i)

-------------------------

----

\

/ num(Site_a,sub_j)

----

all j

ii) n-block normalized sin: FNSI

num(Site_a,sub_i) = sin(theta(Site_a,sub_i))^2

lam(Site_a,sub_i) = num(Site_a,sub_i)

-----------------------------

----

\

/ num(Site_a,sub_j)

----

all j

iii) 2-block exponential: F2EX (based on the logistic function)

lam(Site_a,sub_1) = exp(theta(Site_a)) / [ 1.0 + exp(theta(Site_a)) ]

lam(Site_a,sub_2) = 1.0 / [ 1.0 + exp(theta(Site_a)) ]

iv) 2-block sin: F2SI (based on constant pH-MD and theta-dynamics)

lam(Site_a,sub_1) = sin(theta(Site_a))^2

lam(Site_a,sub_2) = 1.0 - sin(theta(Site_a))^2

v) Fixed lambdas: FFIX (lambda doesn't move from its starting value)

Useful for doing FEP or MBAR in systems set up for MSLD

The MSMA keyword is the Multi-Site lambda-dynamics equivalent to the

LDMAtrix command and will automatically map the input lambda values

onto the coefficient matrix of the interaction energies (and forces)

between blocks.

Assuming that groups of atoms have already been defined to correspond to

"site1sub1" etc., here is an example of a Multi-Site lambda-dynamics

setup in an input file.

BLOCK 7

Call 2 sele site1sub1 end

Call 3 sele site1sub2 end

Call 4 sele site2sub1 end

Call 5 sele site2sub2 end

Call 6 sele site2sub3 end

Call 7 sele site2sub4 end

qldm theta

lang temp 310.0

ldin 1 1.0 0.0 12.0 0.0 5.0

ldin 2 0.50 0.0 12.0 0.0 5.0

ldin 3 0.50 0.0 12.0 3.2 5.0

ldin 4 0.30 0.0 12.0 0.0 5.0

ldin 5 0.40 0.0 12.0 -0.5 5.0

ldin 6 0.15 0.0 12.0 8.5 5.0

ldin 7 0.15 0.0 12.0 15.1 5.0

rmla bond thet

msld 0 1 1 2 2 2 2 fnex 5.5

msma

END

After this setup, minimizations and dynamics can be invoked as usual. MSLD

is currently only compatible with the default dynamics routine (leapfrog

Verlet) and can be used with Langevin dynamics (LANG) using the LEAP

integrator.

Analysis of the generated lambda trajectories can be performed using

options in the trajectory command for multiple blocks at one or two Sites

(see TRAJ LAMB in dynamc.info). For hybrid molecules that have multiple

blocks at more than two Sites, we suggest running the TRAJ LAMB command

with the "print" option to write out lambda and theta values at each step.

Currently, Multi-Site lambda-dynamics is compatible with LDBI and

LDBV. However, the LDBV defined biases are not yet taken into

account in the TRAJ analysis routine.

1) BLOCk [int] enters the block facility. The optional integer is

only read when the block structure is initialized (usually the first

call to block of a run) to specify the number of blocks for space

allocation. If not specified, the default of three is assumed.

2) END exits the block facility. The assignment of blocks, the

coefficient weighting of the energy function, the force/noforce

option, etc. remain in place. For the terms of the energy function

that are supported, each call to ENERGY (either directly or through

MINIMIZE, DYNAMICS, etc. commands) results in an energy and force

weighted as specified. The matrix of interaction coefficients is

printed upon exiting.

3) CALL removes the atoms specified by "atom-selection" from their

current block and assigns them to the block number specified by the

integer. Initially all atoms are assigned to block 1. If atoms are

removed from any block other than block 1, a warning message is

issued. If blocks are assigned such that some energy terms (theta,

phi, or imphi) are interactions between more than two blocks, a

warning is issued when the END command is encountered. (Take such

warnings seriously; this is a severe error and indicates that

something is wrong. However, the problem might be not the CALL

statement (or the atom selection) itself; quite possibly your hybrid

molecule was generated improperly)

4) LAMBda sets the value of lambda to "real". This command is only

valid when there are three blocks active. Otherwise multiple COEF

commands may be used to set the interaction coefficients manually.

LAMBda x

is equivalent to (let y=1.0-x)

COEF 1 1 1.0

COEF 1 2 y

COEF 1 3 x

COEF 2 2 y

COEF 2 3 0.0

COEF 3 3 x

5) COEF sets the interaction coefficient between two blocks (represented

by the integers) to a value (the real number). When the block facility

is invoked, all of the atoms are initially assigned to block 1 and all

interaction coefficients are set to one. The required real value

(first specified) scales all energy terms expect those specific terms

which are named with alternative corresponding scale factors.

The name "VDWA" and "VDWR" correspond to the Attractive and Repulsive

terms in the Lennard-Jones potential respectively. That is they allow

one to independently scale the attractive (r^(6)) and repulsive terms (r^(12))

independently.

6) NOFOrce specifies that in subsequent energy calculations, the

forces are not required. This is economical when using the

post-processing commands (FREE,EAVG,COMP). Forces may be turned back

on with the FORCe command; this is necessary before running

minimizations and dynamics if there was a prior NOFO command.

7) FREE calculates a free energy change using simple exponential

averaging, i.e. the "exponential formula". If the old and new lambdas

(OLDL,NEWL) are specified (can only be done when three blocks are

active), the perturbation energy is calculated for these values (i.e.

FREE gives you the free energy difference between NEWLambda and

OLDLambda via perturbation from the lambda value at which your

trajectory was calculated. If not, the current coefficient matrix is

used (FREE should be used with three blocks, and the use of OLDL and

NEWL is recommended). FIRSt_unit, NUNIt, BEGIn, STOP, and SKIP

specify the trajectory/ies that is/are to be read (for a further

description see the TRAJ command elsewhere in the CHARMM

documentation). TEMPerature defaults to 300 K and gives the

temperature value to be used in k_B*T. CONTinuous specifies the

interval for writing cumulative free energies. A negative value

causes binned (rather than cumulative average) values to be written.

Be careful to make sure that you use correct non-bonded lists (see the

hints section!)

8) INITialize is called automatically when the BLOCK facility is

first entered and may also be called manually at some other point.

All atoms are assigned to block one and all interaction coefficients

are set to their initial value.

9) CLEAr removes all traces of the use of the BLOCK facility. The

next command should generally be END, and then CHARMM will operate

as if BLOCK had not ever been called.

10) EAVG The average value of the potential energy during a simulation

can be calculated with the EAVG (Energy_AVeraGe) command. The parsing

is very much like the FREE command above. The most frequent use of

this command is to calculate the average value of dV/dlambda during

the course of a simulation for use in thermodynamic integration.

CONTinuous specifies the interval for writing cumulative free

energies. A negative value causes binned (rather than cumulative

average) values to be written. Be careful to make sure that you use

correct non-bonded lists (see the hints section!) The command accepts

the OLDL / NEWL option, similarly to FREE, but for EAVG it is

recommended to set up the interaction matrix (using COEF commands)

yourself -- see the hints section.

11) [COMP] The COMP module is essentially a modified version of the

EAVG module which aside from calculating <dU/dl> = <U_1 - U_0> at a

given value of lambda l(i) will also give you expectation values of

this quantity at l(i+-1), l(i+-2) etc. based on perturbation theory.

COMP requires 4 blocks. Put the usual WT (reactant) in block 2 and

MUT (product) in block 3. Put the portion of the environment whose

contribution to the free energy change is desired into block 4 (this

can be everything else, or just a subset) (Note that the same can be

achieved easily with the EAVG command) You have to set up your own

coefficient matrix. Much of the parsing is like the EAVG command.

CONT is not supported. Two special subcommands (required) are DELL

and NDEL. The normal output of COMP is <U_1 - U_0> evaluated at the

lambda of the simulation. However, COMP also evaluates the same

ensemble averages perturbed to lambda = lambda +/-

{0,1,2,...NDEL}*DELL. This (sometimes) helps the quadrature in

thermodynamic integration. Note that NDEL must be at least 1, and

DELL should not be zero. (You have to specify these values; the

default values will lead to an invalid input, i.e. you bomb...) Be

careful to make sure that you use correct non-bonded lists (see the

hints section!) A word of warning: If your initial ensemble average

(at the lambda of the simulation) is not well converged, then your

perturbed values are most likely random numbers. The approach taken

by COMP is theoretically sound, but it should only be applied if

convergence has been established! The output format of COMP is

somewhat messy: COMP first prints <dU/dl> = <U_1 - U_0> at lambda =

lambda - NDEL*DELL

lambda - (NDEL-1)*DELL

...

lambda

lambda + DELL

...

lambda + NDEL*DELL;

then it prints an average (integral) value over these results. The

meaning of this last value is unclear to me. In earlier versions of

this documentation, COMP has been recommended over EAVG. In my

experience the opposite is true. There is little COMP can do which

you can't do with EAVG (aside from obtaining expectation values for

dU/dl). (Maybe the unclear output of the COMP module is the main

reason why I don't like it).

12) [AVER] The AVERage command is used to extract ensemble average

structural properties from a dynamics simulation. Features in this

implementation allow averages taken over ensembles that are perturbed

from that which the simulation corresponds to. This is particularly

useful for calculating the average structure expected at lambda=0.0

from a simulation run at lambda=0.1, for example. One may calculate

average structures [STRUcture] and average distances [DISTance int

int; where the two integers are the atom numbers between which the

average distance is requested], currently. The PERT keyword indicates

that a perturbed ensemble from the dynamics trajectory is desired,

with TEMPerature giving the temperature to use in the exponential for

the perturbation (defaults to 300 K), OLDLambda and NEWLambda are the

lambdas for which the simulation was run and for which the ensemble is

requested, respectively (only valid if three blocks are active; if

these are not specified, the perturbation energy is calculated with

the current coefficient matrix), and the remaining keywords are used

to specify the trajectory. NOTE: TO THE BEST OF MY KNOWLEDGE THIS

COMMAND HAS NOT BE MAINTAINED (so you are on your own if you use it!)

12a) [EXCL] The EXCLusion command allows you to create exclusions between

and within blocks, and thus eliminates the need to add them to the

residue/patch definitions in the rtf. For example, one can exclude

the non-bonded interactions between block i and blok j, as defined

by the block selections from call i {selection} and call j {selection},

with the block subcommand:

EXCL i j

where i and j are the integers corresponding to the blocks i and j,

respectively. This is, in principle, a powerful way to set up

interesting non-bonded exclusions, but was designed primarily for use

with multi-site lambda dynamics to eliminate the need to add the

long list of multiple-site exclusions to the rtf residue and patch residue

definitions. For examples of the use of this command, see:

c41test/blockexcl_test.inp and c41test/msld_test2.inp.

[ADEX] The ADEXclusion command adds to the list of exclusions created

with the EXCLusion command. (EXCLusion overwrites previous exclusions

when called a second time.) This enables the automated setup of

exclusions in a loop, when the number of exclusions is too large to

fit on a single charmm script input line.

13) LDINitialize specifies input parameters for running lambda

dynamics. It sets up the value of lambda**2, the velocity of

the lambda, its mass and reference free energy (or biasing potential).

E.g, the following input lines set up

parameters for the third lambda with [lambda(3)]**2 = 0.4,

lambdaV(3) = 0.0, lambdaM(3) = 20.0, and lambdaF(3)=5.0 (note that lambdaF(1)

should always be set to zero).

LDIN 3 0.4 0.0 20.0 5.0

For more details, see Node Hints, section "lambda-dynamics simulations".

14) LDMAtrix will automatically map the input lambda**2 values onto the

coefficient matrix of the interaction energies (and forces) between

blocks.

15) LDBI provides an option on applying biasing potentials on lambda

variables. The integer value specifies the total number of biasing

potentials to be used. E.g,

LDBI 3

will include total of 3 biasing potentials in the simulation.

16) LDBV sets up the specific form of the biasing potentials. At the

moment, the functional form is of power law and allows three different

classes (for details see "the actual simulations"). The input format is

LDBV INDEX I J CLASS REF CFORCE NPOWER

e.g.

LDBV 2 2 3 3 0.0 50.0 4

will assign the second biasing potential acting between lambda(2) and

lambda(3). The potential form belongs to the third class with reference

value of zero, the force constant of 50 kcal/mol and the power of four.

*) THBV uses theta biasing during MSLD theta dynamics to reduce the

amount of time spent sampling alchemical intermediates which allows

simulations with increased numbers of substituents. Two theta biases

are available, a collective bias (COLL)

nhigh(s) = sum((0.5*sin(theta(s,i))+0.5)**POWER,i)

nlow(s) = sum((-0.5*sin(theta(s,i))+0.5)**POWER,i)

V = 0.5*COEF*((nhigh(s)-1)**2+(nlow(s)-nsub(s)+1)**2)

where s and i are site and substituent indices, respectively; and an

independent bias (INDE)

V = sum(-b(-0.5*sin(theta(s,i))+0.5)^4,i)

with a default b coefficient of b=B*kT

B = 0.5*ln(0.125*pi*Ns^2*B)

The second argument of THBV chooses the collective bias or the independent

bias. The third argument specifies a site, by number, or if the keyword ALL

is used, will apply the bias to all sites. For the collecitve bias the

syntax

THBV COLL ALL COEF POWER

will set the coefficient to COEF, (kT is recommended), and will set the

power to POWER (2 is recommended).

For the independent bias, the syntax

THBV INDE ALL AUTO

will set the b value to the defalt value indicated above, and

THBV INDE ALL COEF

will set the coefficient to the real value given by COEF.

17) LDRStart is used to restart the lambda dynamics runs.

18) LDWRite specifies the FORTRAN output unit No. and the frequency

for writing lambda histogram by assigning an integer to IUNL and an

integer to NSAVL. (IUNL and NSAVL can be reset in DYNAmic command,

see

**»**dynamc )19) RMBOnd and RMANgle are used when no scaling of bond and angle energy

terms is desired.

20) RMLA is used when no scaling of bond, angle, proper torsion, and

improper torsion terms are desired. This option always works with block module.

The keywords: "RMBOnd" and "RMANgle" work only in lambda-dynamics.

COEF command can work in the same way when lambda-dynamics or hybrid-MC/MD are

not used.

e.g.

"RMLA BOND" = "COEF real BOND 1.0"

RMLA BOND removes scaling for both normal bond and Urey Bradley bond terms.

Use RMLA 12BOnd to remove bond scaling only and 13BOnd to remove Urey

Bradley scaling only.

21) SAVE saves the decomposed-energy file for post processing in the TSM

module. This command gives a choice for free energy calculation with

block module to get free energy without saving the trajectory file.

The condition and the name for the decomposed-energy file can be defined

in the dynamics module. (» dynamic keyword: IBLC, NBLC)

22) UNSAve removes the traces of the use of SAVE command shown above.

23) QLDM turns on lambda-dynamics option. LDIN command also turns on

the lambda-dynamics option only when QLMC turns off.

24) QLMC turns on hybrid-MC/MD option. If QLMC option is on, LDIN commands

do not activate the QLDM option.

In this version, we do not re-assign the velocity of the atoms when

chemical variables (lambda) are changed by MC method. Therefore, the kinetic

terms suddenly change into the different phase space. The stochastic dynamics

may diminish such artificial effects and help to reach the canonical ensemble.

QLMC and QLDM are exclusive and latest choice is active.

QLMC command should specify conditions for hybrid-MC/MD.

e.g.

QLMC MCTEmperature 300.0 FREQ 10 MCST 5 MAX 0.9

IN the above example, the temperature used for sampling the chemical space

by MC method is 300.0 [Kelvin]; MC sampling works every 10 molecular dynamics

steps (using for sampling of the atomic space); in one MC sampling, 5 trials

are examined; the scale factor (lambda^2) for the selected ligand is assigned

to 0.9 and the rest of ligands (L-1) have the scale factor 0.1/(L-1).

Different temperature can be defined in the lambda-dynamics and hybrid MC-MD

for atomic variables and chemical variables.

25) MCIN allows the intermediate states in which only two ligands have non-zero

lambda values in hybrid-MC/MD method.

e.g. (Three ligands system)

MCIN 5 0.0 0.25 0.5 0.75 1.0

5 means that each ligand may have one these five scalings:

0.0, 0.25, 0.5, 0.75, and 1.0.

In this condition, CHARMM recognizes the following chemical states:

(SCALE FACTOR)

STATE NO. LIG_A LIG_B LIG_C

1 1.0 0.0 0.0

2 0.0 1.0 0.0

3 0.0 0.0 1.0

4 0.25 0.75 0.0

5 0.75 0.25 0.0

6 0.25 0.0 0.75

7 0.75 0.0 0.25

8 0.0 0.25 0.75

9 0.0 0.75 0.25

10 0.5 0.5 0.0

11 0.5 0.0 0.5

12 0.0 0.5 0.5

26) MCDI (increment) specifies the step size to move in lambda chemical

movement. It allows intermediate states in which more than two ligands

can have non-zero lambda values in hybrid-MC/MD method. "MCDI" requires the

uniform interval for the definitions of the intermediate states.

Step size must satisfy:

Stepsize = 1.0/integer.

Example: Three ligands system

MCDI 0.25 ! 0.25 shows the step size to move in lambda chemical movement.

In this condition, CHARMM recognizes next chemical states.

(SCLE FACTOR)

STATE NO. LIG_A LIG_B LIG_C

1 1.0 0.0 0.0

2 0.0 1.0 0.0

3 0.0 0.0 1.0

4 0.25 0.75 0.0

5 0.75 0.25 0.0

6 0.25 0.0 0.75

7 0.75 0.0 0.25

8 0.0 0.25 0.75

9 0.0 0.75 0.25

10 0.5 0.5 0.0

11 0.5 0.0 0.5

12 0.0 0.5 0.5

13* 0.25 0.25 0.5

14* 0.25 0.5 0.25

15* 0.5 0.25 0.25

It is possible for MCDI to produce a state in which three ligands take

non-zero lambda values as shown with the asterisk (states 13, 14 and 15).

"MCDI" seems to be more general, but "MCIN" allows non-uniform

intervals. Thus, small step sizes can be assigned near end points.

27) MCRS ignores the force for lambda coming from the restraining potential

in lambda-dynamics. It also ignores the restraining potential energy when

chemical space is sampled by MC method. CMC/MD (Chemical Monte Carlo &

molecular dynamics) method can be carried out by combining this command

with QLMC.

28) MCLEar removes the traces of the use of QLMC command shown above.

BLOCK CLEAr command also removes the all traces of the use of QLMC.

MCLEar removes the traces of QLMC, while BLOCK CLEar removes all traces of the

BLOCK module.

29) LANG turns on the interaction between lambda variable and langevin

heatbath. In general, weak interaction between lambda variables and atoms

produced large deviations from the target temperature. Different temperatures

for lambda and atoms make nonequilibrium states and gave incorrect free

energies. Therefore, we recommend that LANG turn on in any lambda-dynamics

simulations. LEAP FROG integration method is required when using the LANG

option.

30) RSTP adds the restraining potential for the unbound states ligands

in lambda-dynamics and hybrid-MC/MD method to keep the physical low energy

states. The type of the restraining potential used with RSTP is;

R = alpha *(1 - lambda^2)* ( V - F )

i i i i

It disappears when this ligands is in bound state (lambda=1).

e.g.

REST 3 0.3

3 means the type of the restraining potential; 0.3 shows the alpha value.

There are three types for the restraining potential.

Type 1 Both environmental atoms and the ligands feel the restraining potential.

Umbrella sampling technique is used to remove the bias effect coming

from the restraining potential.

Type 2 The fixed average structure of the environmental atoms are assigned into

Block 2. The restraining potential was calculated Ri is defined as a

function of the fixed environmental atoms and the ligands.

When the system is flexible and the difference between the real

coordinates of the environmental atoms and fixed average coordinates

are considerably large, the convergence tends to slow.

Type 3 When the environmental atoms form the specific structure and vibrated

around the minimum, the fixed average structure of the environmental

atoms are similar to those of the real time coordinates.

Therefore, the force coming from the restraining potential can be

approximated zero as an average. If such a condition is satisfied,

the environmental atoms can be ignored the force coming from the

restraining potential and the ligands only feel the restraining

potential.This approximation may have a problem when we handle the

unstructured system like gas or liquid.

The utility program, post_ldm_mcmd.exe is prepared for calculating the free

energy differenes both without or with the restraining potential in

lambda-dynamics or hybrid-MC/MD method.

This program is saved in "support/post_analysis".

31) MCFRee EXFReq int FINI real FFIN real FLAT real is the main subcommand for

the definition of simulated scaling simulations. Here, EXFReq int is to set up

the frequency for Monte Carlo acceptance and rejection of the lambda space

move. FINI real is to set up the initial modification factor, usually as

2.71828 following the original Wang-Landau algorithm. FFIN real is to set up

the cutoff value for the final modification factor. FLAT real is to set up

the cutoff value for each cycle of flatness judgment.

Reference: Li, H., Fajer, M., and Yang, W. 2007. Simulated scaling method for

efficient localized conformational sampling and simultaneous alchemical free

energy simulation: A general method for MM, QM, and QM/MM simulations.

J. Chem. Phys. 126:024106.

32) MCLAmd int LAMD0 real LAMD1 real ...... LAMD[int-1] real is an additional

facility for the flexible usage of the simulated scaling method. Here, [int]

is to define the number of lambda values. LAMD0 is the first lambda value,

LAMD1 is the second one, ...., LAMD[int-1] is the last one.

33) HYBH , HYBrid_Hamiltonian module. Implementation of the truncation

scheme described in "Ensemble Variance in Free Energy Calculations by

Thermodynamic Integration: Theory, Optimal "Alchemical" Path, and

Practical Solutions", A.Blondel (2004) J.Comp.Chem 25, 985-993.

Details on the method should be sought therein. In brief, the

implementation is based on dual topology (although single topology

could be used under some conditions), the bonded terms (bond, angle

and Urey-Bradly) are kept unchanged, dihedral and impropers are

modified according to simple quadratic scheme (w_product=(3.l+1).l/4),

and electrostatic and van der Waals are treated together with a

truncation scheme reminiscent of soft-core vdw to minimize the

numerical fluctuations of the integrant (hence Optimal "Alchemical"

Path). Ewald sums and correction terms associated appeared soft

enough to be treated according to linear scaling of the charges,

allowing direct analytical calculation of dEwald/dl. A benefit of the

method, in addition to the fact that the integrant has limited

numerical fluctuations, is that it also produce a linear evolution of

the integrant along lambda (or l) in regular cases.

The implementation attempts to supports most of non-bonds, image

and Ewald sums options and warnings are made. Slow routines are not

currently supported. However, it is advised to test the results when

new combination of options are used. CMAP is not currently supported.

Associated commands are called from within the BLOCk module and are:

HBYH real: Switchs the module on and sets the lambda parameter.

Due to the theoretical properties of the method, evenly spaced

values should be sufficient (eg. l=(2i-1)/20). The product part

(bloc 3) is weighted according to l as explained above, and the

reactant part (bloc 2) is weighted according to (1-l) as explained

above.

OUTH int: Sets the output unit for the dE/dl terms.

TSTH real [<update-spec>]: Sets dl and tests the derivatives (dE/dl)

by finite differences (E(l+dl)-E(l-dl))/2/dl. None zero components

of the energy are printed.

PRIN : Prints dE/dl with the usual ENERGY printing format.

PRDH : Writes dE/dlambda components to outh unit. Replaces the

automatic writting performed during dynamics, for example, when

re-reading a trajectory for post-processing.

The current form of the output is formatted, two line per dynamic step.

R l dDIHEr dIMDIHEr dVDWr dELECr dEWKSUMr dEWSELFr d(EWEXCL+EWQCOR+EWUTIL)r

P l dDIHEp dIMDIHEp dVDWp dELECp dEWKSUMp dEWSELFp d(EWEXCL+EWQCOR+EWUTIL)p

Format: (a1,1x,f6.4,7(1x,1pg24.16e2))

CLHH: Clears the data structure for truncation scheme and switchs off

the module without changing the rest of the block setup. Note, the

BLOCk/CLEAr command also switchs off the module.

No analysis routine is currently supplied as careful convergence

analysis should be undertaken. It is advised that additions of the

terms be made at least in real*8 format as truncation errors might

be significant otherwise.

Testcases c35test/block_hybh.inp & block_hybh_ew.inp are provided.

34) MSLD invokes Multi-Site lambda-dynamics. The integers which follow

the keyword indicate the "Site" to which atoms within each block are

assigned. The first block must be assigned to Site 0 (the "environment"

atoms). Currently, QLDM THETA must be specified prior to invoking MSLD.

If there are too many blocks to assign each to a site in the MSLD

command, (due to CHARMM variable and line length limitations),

MSLD may be invoked with the NSITe option, e.g. "MSLD NSITe int",

where int specifies the number of sites, and blocks may be assigned

to sites individually later in the block section using

"BLASsign int_block int_site", which assigns block int_block to site

int_site.

Several different functional forms of lambda have been implemented. The

default functional form is FNEX 5.5. (Note: these functions are for

lambdas associated with all blocks except for block 1--ie. the environment

atoms at site 0.)

i) n-block normalized exponential: FNEX [c]

Note: Use FNXS [c1 c2 ... cnsites] to set a different c for each site

num(Site_a,sub_i) = exp(c*sin(theta(Site_a,sub_i))

lam(Site_a,sub_i) = num(Site_a,sub_i)

-------------------------

----

\

/ num(Site_a,sub_j)

----

all j

ii) n-block normalized sin: FNSI

num(Site_a,sub_i) = sin(theta(Site_a,sub_i))^2

lam(Site_a,sub_i) = num(Site_a,sub_i)

-----------------------------

----

\

/ num(Site_a,sub_j)

----

all j

iii) 2-block exponential: F2EX (based on the logistic function)

lam(Site_a,sub_1) = exp(theta(Site_a)) / [ 1.0 + exp(theta(Site_a)) ]

lam(Site_a,sub_2) = 1.0 / [ 1.0 + exp(theta(Site_a)) ]

iv) 2-block sin: F2SI (based on constant pH-MD and theta-dynamics)

lam(Site_a,sub_1) = sin(theta(Site_a))^2

lam(Site_a,sub_2) = 1.0 - sin(theta(Site_a))^2

v) Fixed lambdas: FFIX (lambda doesn't move from its starting value)

Useful for doing FEP or MBAR in systems set up for MSLD

The MSMA keyword is the Multi-Site lambda-dynamics equivalent to the

LDMAtrix command and will automatically map the input lambda values

onto the coefficient matrix of the interaction energies (and forces)

between blocks.

Assuming that groups of atoms have already been defined to correspond to

"site1sub1" etc., here is an example of a Multi-Site lambda-dynamics

setup in an input file.

BLOCK 7

Call 2 sele site1sub1 end

Call 3 sele site1sub2 end

Call 4 sele site2sub1 end

Call 5 sele site2sub2 end

Call 6 sele site2sub3 end

Call 7 sele site2sub4 end

qldm theta

lang temp 310.0

ldin 1 1.0 0.0 12.0 0.0 5.0

ldin 2 0.50 0.0 12.0 0.0 5.0

ldin 3 0.50 0.0 12.0 3.2 5.0

ldin 4 0.30 0.0 12.0 0.0 5.0

ldin 5 0.40 0.0 12.0 -0.5 5.0

ldin 6 0.15 0.0 12.0 8.5 5.0

ldin 7 0.15 0.0 12.0 15.1 5.0

rmla bond thet

msld 0 1 1 2 2 2 2 fnex 5.5

msma

END

After this setup, minimizations and dynamics can be invoked as usual. MSLD

is currently only compatible with the default dynamics routine (leapfrog

Verlet) and can be used with Langevin dynamics (LANG) using the LEAP

integrator.

Analysis of the generated lambda trajectories can be performed using

options in the trajectory command for multiple blocks at one or two Sites

(see TRAJ LAMB in dynamc.info). For hybrid molecules that have multiple

blocks at more than two Sites, we suggest running the TRAJ LAMB command

with the "print" option to write out lambda and theta values at each step.

Currently, Multi-Site lambda-dynamics is compatible with LDBI and

LDBV. However, the LDBV defined biases are not yet taken into

account in the TRAJ analysis routine.

Top

A warning is in order: the BLOCK module is quite user-unfriendly, AND

the user (=you) has to know what he/she is doing, otherwise you won't

get anywhere! (Of course, this could be a blessing in disguise) There

are two applications for BLOCK: (i) Mere use as an energy partitioning

facility, which may, e.g., very helpful as an alternative to the

INTEraction energy command and (ii) use in free energy simulations.

The focus here is on free energy applications. The following paragraphs

assume that you are familiar with the theory of free energy difference

simulations (e.g. Brooks et al. Advances in Chem. Physics, Vol. LXXI,

1988, chapter V); the emphasis here is to show how a rough tool as

BLOCK can be used to implement the theory in a program and (of course)

how to use it.

Using BLOCK in order to calculate a free energy difference consists

out of two rather dissimilar parts (as far as practical problems are

concerned): (i) Run your system at various values of lambda and save

trajectories. (ii) Postprocess the trajectories with the FREE or the

EAVG command (possibly COMP), use the quantities which these modules

give you to calculate the free energy difference.

(i) The actual simulations

==========================

It's probably easiest to use a concrete example, and the free energy

difference between ethane and methanol in aqueous solution is used for

that purpose. BLOCK is a so-called dual topology method (D. Pearlman,

JPC 1994, 98, 1487) i.e. one has to duplicate any atom that is

different with respect to any of its parameters. In the

ethane/methanol case this means that you have to run with a solute

which looks something like

H1

\ /H4

\ C1E ---- C2-H5

H2 = { } \H6

/ C1M --- OG

/ \HG1

H3

(and there is water.)

Conceptually, this system is divided into three regions:

environment: water, H1, H2, H3 (the region where nothing changes)

reactant: C1E, C2, H4, H5, H6 (ethane half)

product: C1M, OG, HG1 (methanol half),

where of course the role of reactant and product is interchangeable.

The steps involved to start running dynamics are as follows:

(1) set up the hybrid (generate psf). In principle straightforward,

but there is a practical pitfall: The autogenerate angles and

dihedrals option(s) may produce artificial dihedrals/angles between

the two/three parts of the system, e.g. you don't want angles

H1-C1E-OG etc. or dihedrals H3-C1M-C2-H4 etc. Also, make sure to

specify nonbonded exclusions between the reactant and product part,

otherwise you'll get endless distance warnings and may even bomb if

two atom positions coincide.

(2) Place the hybrid into water (stochastic or periodic boundary

conditions -- yes, IMAGE is now supported) as usual

(3) Partition the system, i.e. enter BLOCK

The following script fragment will do the trick:

block 3

call 2 sele <reactant> end

call 3 sele <product> end

end

(reactant and product have to be defined according to your system).

BLOCK 3 initializes the block module with 3 blocks, all atoms are in

block 1. The two CALL commands bring the reactant and product part of

the system into block 2 and 3 respectively.

(4) Run the necessary MD simulations. Let's assume that you decide to

use the following values of lambda, lambda = 0.1, 0.3, 0.5, 0.7, 0.9.

You want to start your simulation at lambda = 0.1 and you have already

partitioned your system as shown in (3). (This information is kept

within the same script between calls to block, but it is not saved in

restart files or the psf, i.e. you have to repeat this step (as well

as step (3)) in every input file). Enter block again, e.g.

block

lamb 0.1

end

From now on interactions between the 3 blocks will be scaled according

to the following matrix (lambda = l = 0.1 ==> 1-l = 0.9):

block | 1 2 3

------|--------------------

1 | 1.0 1-l l

2 | 1-l 1-l 0.

3 | l 0. l

Please note that BLOCK will first calculate an interaction, then check

to which block the two atoms belong and scale the energy (and forces)

appropriately. Therefore, if the distance between 2 atoms is zero

(e.g. in the ethane/methanol example I would define C1M and C1E on top

of each other!) then you need non-bonded exclusions, otherwise you

encounter a division by 0 error!

The LAMB command is a shortcut for the following sequence of COEF

commands, the following code fragment should be self-explanatory:

block

coef 1 1 1.0

coef 1 2 0.9

coef 1 3 0.1

coef 2 2 0.9

coef 2 3 0.0

coef 3 3 0.1

end

BLOCK only accepts and uses symmetric matrices, i.e. it doesn't

matter whether you specify COEF 1 2 or COEF 2 1.

Whenever you now call the energy routines, the energies/forces

returned from them will be scaled according to the matrix you have set

up. Minimizers and Dynamics can be used as always. So you are ready

to run dynamics, and for arguments sake say that you run at every

value of lambda 10,000 steps equilibration and 20,000 steps production

(i.e. you save coordinates to trajectories) You don't need to save

every step, every 5th to 20th step is probably more than enough. (If

you saved every step you'd obtain highly correlated data, i.e. you

have larger trajectories, but you won't gain anything in terms of

convergence.)

(ii) Post-processing -- how to obtain a free energy difference

==============================================================

At this point in our example, you would have five trajectories

corresponding to lambda = 0.1, 0.3, ..., 0.9 The BLOCK module now has

to be used to obtain the average quantities you need for either the

exponential formula (FREE) or thermodynamic integration (EAVG,COMP)

from the trajectories you generated in step (i)

(1) At this point, some issues regarding the non-bonded list have to

be considered. No special considerations were necessary while running

dynamics (aside from having some non-bonded exclusions where

necessary); you just set up list updates as usual. During

post-processing there are two considerations: (a) efficiency -- you

just want to calculate the necessary subset of interactions (otherwise

your post-processing run will take about as much time as the

simulation itself), and (b) proper list-updating.

(a) Efficiency: In none of the post-processing routines do you need

the interactions between particles that belong to the environment;

therefore you should avoid calculating them. This can be done easily

by specifying

cons fix sele <environment> end

Note that this is not necessary, but it will reduce the CPU time

necessary from hours to minutes (and results are identical!) However,

if you had atoms belonging to reactant or product or both FIXed during

the simulations in step (i), you MUST NOT FIX them now; otherwise

you'll omit contributions.

(b) List updating: While the efficiency considerations in principle

are optional, you have to follow one of the two strategies below

otherwise you'll get erroneous results. If you used IMAGE, you have

to use the second protocol! Originally, the BLOCK post-processing

commands would not do any list updating. This meant that you had to

have a nonbonded list which would include all possible interactions

before starting post-processing -- don't forget that you post-process

over, e.g., 20 ps and particles will move quite far. You can easily

create such a nonbonded list by specifying a CUTNB value of, e.g. 99.

or 999. Ang (surely, all possible interactions will be included). A

!set up system (psf, initial coordinates)

block

!partition system

end

cons fix sele <environment> end

==> energy cutnb 99. <all other options as during dynamics>

!open trajectories

block

!postprocessing

end

In this case, do not use the inbf, ihbf and imgf options of the

post-processing commands, they will default to 0, i.e. no update.

This approach, however, CANNOT work with IMAGES! Proper use of IMAGEs

requires that the minimum image convention is checked periodically,

i.e. particles have to be repartitioned between primary and image

region. As the BLOCK post-processing commands now understand INBF,

IHBF and IMGF, this doesn't pose a problem. However, the automated

update is not supported (if you specify a negative value, you'll get a

mild warning and the system will default to +1), and I recommend that

you use 1 for all frequencies (don't forget, the frames in your

trajectory are several steps apart, i.e. in general an update may be

necessary) The above scheme now looks like:

!set up system (psf, initial coordinates)

block

!partition system

end

cons fix sele <environment> end

! set up images if needed

==> energy <all options, incl. CUTNB, as during dynamics>

!open trajectories

block

eavg <other options> inbf 1 ihbf ? (imgf 1)

end

Unless you have explicit hbond terms, ihbf can of course be 0!

(Please note that there may or may not be problems with CRYSTAL, see

Limitations section)

(2) The actual post-processing commands. In the following I'll

explain how to set things up for FREE, EAVG and COMP (as well as why).

To speed up things further, you'll also want to specify the NOFOrce

option at some point.

FREE: This module allows you to calculate the necessary ensemble

average for the exponential formula. Using our example, you can for

example estimate the free energy difference between l=0.1 (a value at

which you ran a trajectory) and l=0.0, or, based on your l=0.1

trajectory the free energy difference between l=0.0 and 0.2 (double

wide sampling), i.e.

A(0.0)-A(0.1) = -k_B*T*ln <exp[-(U(l=0.0)-U(l=0.1))/kT]>_(l=0.1)

or

A(0.2)-A(0.0) = -k_B*T*ln <exp[-(U(l=0.2)-U(l=0.0))/kT]>_(l=0.1)

You should set up your system with 3 blocks and the usual environment,

reactant and product partitions. Before entering block to issue the

free command, you have to open the trajectory/ies.

! all the stuff shown above for non-bond lists

open file unit 10 read name dat01.trj

block

free oldl 0.1 newl 0.0 first 10 nunit 1 [temp 300. -

inbf 1 imgf 1]

end

or, for double wide sampling, the free line would be replaced by

free oldl 0.0 newl 0.2 first 10 nunit 1 [temp 300. -

inbf 1 imgf 1]

Here dat01.trj is the trajectory which contains your 20 ps of dynamics

at lambda = 0.1. Based on the oldl/newl values (which correspond to

A(newl) - A(oldl)), FREE generates the appropriate interaction matrix,

which it prints; I recommend that you try to understand why it

generates this matrix! FIRST is the unit number of the first

trajectory file (10 in our example), NUNIT is the number of

trajectories (1 in our example). These (and the other options

regarding the trajectories work as in any other post-processing

command in CHARMM, see e.g. the TRAJ command) The update frequencies

are optional depending on how you decided to handle your non-bonded

updates. temp defaults to T=300 K, cf. equations above.

If you specify CONT +n, you'll get a cumulative average every n steps;

in this case the last value equals the final result; if you specify CONT

-n, you'll get the average over every n frames, plus of course the

final result at the end.

Note that trajectories are not rewound after use; i.e. before any

subsequent FREE (or EAVG,COMP) command you have to rewind (or reopen)

them!

Once you have all the free energy pieces you need, you simply add them

up to obtain the free energy difference (beware of sign errors

depending on how you defined oldl/newl)

EAVG: The main use of this module lies in obtaining the required

ensemble averages for thermodynamic integration. The most significant

difference to EAVG is that you have to specify your own interactions

matrix. BLOCK uses linear coupling in lambda in the potential energy

function, i.e.

V(l) = V0 + (1-l)*V_reac + l*V_prod,

where V0 contains all the intra-environment terms, V_reac are the

intra-reactant and reactant-env. interactions, and V_prod are the

intra-product and product-env. interactions, respectively. The

quantity of interest in TI is dV/dl; for the above potential energy

function we have

dV/dl = V_prod - V_reac

It's very easy to obtain this quantity from EAVG. Use 3 blocks,

partition the system as before.

! all the stuff shown above for non-bond lists

open file unit 10 read name dat01.trj

block

coef 1 1 0.

coef 1 2 -1.

coef 2 2 -1.

coef 1 3 1.

coef 2 3 0.

coef 3 3 1.

eavg first 10 nunit 1 [inbf 1 imgf 1 cont +-n]

end

You will calculate the average interaction energy over all the frames

in the trajectory according to the following (symmetric) matrix

0.0

-1.0 -1.0

1.0 0.0 1.0;

i.e. it's easy to see that the above script will give you <V_prod -

V_reac>_(l=0.1). If you post-process the other trajectories (l=0.3,

0.5, ..,0.9) in an analogous fashion, you just have to approximate the

TI integral by the trapezoidal formula (for basic Newton Cotes

formulae (open and closed) see, e.g., Numerical Recipes), i.e. in this

case you would have

dA = 0.2 * (dV(0.1)+dV(0.3)+...+dV(0.9)),

where dV(0.1) = <V_prod - V_reac>_(l=0.1), etc.

The above is an example of the basic use of EAVG. You automatically

get the formal components according to interaction type. Cont +-n

works similarly to the FREE case. If you wanted to exclude the

intramolecular contributions from ethane and methanol you could set up

a slightly different coefficient matrix, i.e.

coef 1 1 0.

coef 1 2 -1.

coef 2 2 0.

coef 1 3 1.

coef 2 3 0.

coef 3 3 0.

and you'll get only the solute-solvent contributions. You can use

more blocks (m > 3) to extract only a subset of interactions, e.g.

block 1: environment - x

block 2: reactant

block 3: product

block 4: x,

where x is the region of interest, e.g. a specific sidechain in a

protein (but not the one that is mutated!)

Using EAVG with an appropriate coefficient matrix, e.g.

coef 1 1 0.

coef 1 2 0.

coef 1 3 0.

coef 1 4 0.

coef 2 2 0.

coef 2 3 0.

coef 2 4 -1.

coef 3 3 0.

coef 3 4 1.

coef 4 4 0.

will give you (after integration over lambda) the free energy

contribution of the interaction of sidechain x with the mutation site.

Note that such formal free energy components may be (strongly)

path-dependent. These last two examples have hopefully provided a

flavor of what can be done with the EAVG module.

COMP: This module is also used for thermodynamic integration. It

always operates with four (and only four) blocks, just as the advanced

example last given for EAVG, so it facilitates COMPonent analysis.

Here I want to focus on the second unique aspect of COMP, it's

capability to extrapolate additional datapoints, and so I consider in

the framework of our ethane/methanol example the "special" case where

I want the total free energy difference (as before in EAVG). In order

to do this, the system needs to be partitioned as follows

block 1: --

block 2: reactant

block 3: product

block 4: environment

Whereas EAVG gave us <V_prod - V_reac>_l only for those lambda values

at which we had actually done the simulations, COMP gives us

additional values via perturbation (see Bruce Tidor's thesis). Using

! all the stuff shown above for non-bond lists

open file unit 10 read name dat01.trj

block

coef 1 1 0.

coef 1 2 0.

coef 1 3 0.

coef 1 4 0.

coef 2 2 -1.

coef 2 3 0.

coef 2 4 -1.

coef 3 3 1.

coef 3 4 1.

coef 4 4 0.

comp first 10 nunit 1 [inbf 1 imgf 1] dell 0.06667 ndel 1

end

will now give us <V_prod - V_reac>_l at l=0.03334, l=0.1 and

l=0.16667. If we use the same script on the other trajectories, we

have 15 instead of 5 datapoints for the integration, i.e. we can

obtain dA as

dA = 0.06667 * (dV'(0.03334)+dV(0.1)+...+dV'(0.96667)),

where dV(0.1) = <V_prod - V_reac>_(l=0.1), etc. and the ' indicates

that this is a perturbed quantity. In principle, this

should give a better numerical integration; however, in practice

everything depends on how well your actual data (l=0.1, 0.3, ...,0.9)

are converged.

There is no check whether your ndel/dell combination is meaningful;

and you cannot run COMP without using the perturbation feature, i.e.

NDEL should be set to at least 1 (valid values are 1 through 5). The

defaults (if you don't specify ndel/dell) lead to an invalid input

(This should be fixed...)

(iii) Lambda-dynamics simulations

=================================

In an efforts to make the transition from using previous subcommands

to running the lambda dynamics as smoothly as possible, we purposely

parallel new syntax after the COEF subcommand. There are

total of eight new keywords for setting up new dynamics. They are

classified according to their functionality.

(a) LDINitialize and LDMAtrix

These two keywords are basic commands for starting the lambda

dynamics run. The correct use of them is tied together with the BLOCK

and CALL commands. Using the same example as the one given in "the

actual simulations", the input script fragment will be as following:

block 3

call 2 sele <reactant> end

call 3 sele <product> end

LDIN 1 1.0 0.0 20.0 0.0

LDIN 2 0.9 0.0 20.0 0.0

LDIN 3 0.1 0.0 20.0 0.0

LDMA

end

Here, the LDINitialize command models after the COEF command with

the format

LDIN INDEX LAMBDA**2 LAMBDAV LAMBDAM LAMBDAF

Several comments are in order. First, notice that [lambda(1)**2]

= 1.0 and [lambda(2)]**2 + [lambda(3)]**2 = 1.0. They are quite

similar to the inputs of COEF subcommand. However, since one

index instead of a pair is required here, only diagonal elements

of the interaction coefficient matrix are specified. To fill up

the matrix, LDMA is provided to finish the job automatically.

In general, if there is total of N blocks, the first one is

by default assumed to be the region where nothing changes.

Therefore, [lambda(1)**2] = 1.0 is always true. The condition

N

____

\

/ [lambda(i)**2] = 1.0 (1)

----

i = 2

has to be satisfied for the partion of the system Hamiltonian.

Due to some technical reasons in our implementation (details

see PDETAIL.DOC), we have used [lambda(i)**2] instead of lambda(i)

in our partion of the system Hamiltonian. Next, to make sure the above

condition is met at any given simulation step, we have also enforced a

condition containing velocities of the lambda variables

N

____

\

/ lambda(i)*lambdaV(i) = 0.0 (2)

----

i = 2

We used lambdaV(i) = 0.0 in the above script just to simplify the

input. As far as the mass parameter lambdaM is concerned, the minimum

requirement is that the value of mass has to be chosen such that the

time step (or frequency) of lambda variables is consistent with that

used for spatial coordinates x, y, z. Since the lambda variable is

introduced into the system by using extended Lagrangian,

considerations gone into the similar quantities, such as the

adjustable parameter Q in a Nose thermostat are applicable to the

choice of lambdaM. Some crude estimation can be made by examining

the derivative of the system Hamiltonian with respect to the

lambda, the curvature (simple harmonic approximation) or energy

difference between two end-point states (0 and 1). Our experience

has indicated that a conservative choice of the mass, i.e. a little

bit heavier mass than that of the crude estimate, serves us well

so far.

The biasing potential LAMBDAF has two functions: (1) In the screening

calculations LAMBDAF corresponds to the free energy difference of the

ligands in the unbound state. Such calculations can identify ligands

with favorable binding free energy and a ranking of the ligands can be

obtained from the probability of each ligand in the lambda=1 state;

(2) In precise free energy calculations, LAMBDAF corresponds to the best

estimate of free energy from previous calculations. Therefore the

estimate of free energy can be improved iteratively.

(b) LDBI and LDBV

In order to provide better control over simulation efficiency and

sampling space, an option of applying biasing (or umbrella)

potentials is furnished. LDBI specifies how many biasing

potentials will be applied and LDBV supplies all the details.

The general input format is

LDBV INDEX I J CLASS REF CFORCE NPOWER

Let us look at the following script

block

LDBI 3

LDBV 1 2 2 1 0.2 40.0 2

LDBV 2 3 3 2 0.6 50.0 2

LDBV 3 2 3 3 0.0 20.0 2

end

It states that there is total of 3 biasing potentials. The first one

(INDEX = 1) is acting on lambda(2) itself (I = J = 2), the second one

on lambda(3) and the third one is coupling lambda(2) and lambda(3)

together. At the moment, five different classes of functional forms

are supported:

CLASS 1:

__

| CFORCE*(lambda - REF)**NPOWER if lambda < REF

V =|

| 0 otherwise

|__

CLASS 2:

__

| CFORCE*(lambda - REF)**NPOWER if lambda > REF

V =|

| 0 otherwise

|__

CLASS 3:

V = CFORCE*[lambda(I) - lambda(J)]**NPOWER

CLASS 4:

__

| CFORCE*(1.0 - ((lambda - REF)**2)/REF**2) if lambda < REF

V =|

| 0 otherwise

|__

CLASS 5:

V = CFORCE*lambda(I)

note: the CLASS 5 biasing potential is the same as invoking the

biasing potential LAMBDAF in LDIN (except these biases will not

currently be taken into account in the TRAJ analysis routines).

CLASS 6:

V = CFORCE*[lambda(I) * lambda(J)]

CLASS 7:

V = CFORCE*[lambda(I) * (1 - lambda(I))]/[lambda(I) + REF]

CLASS 8:

V = CFORCE*[lambda(I) * lambda(J)]/[lambda(I) + REF]

CLASS 9:

V = CFORCE*[lambda(J) * (1 - ((lambda(I) + REF)/REF)**NPOWER)]

CLASS 10:

V = CFORCE*[lambda(J) * (1 - exp(REF*lambda(I)))]

(c) LDRStart

LDRStart is used only if for some reason, e.g. execution of EXIT command,

the logical variable QLDM for the lambda dynamics has been set to false.

In this case, to restart the dynamics, LDRStart can be used to reset

QLDM = .TRUE.. However, if LDIN is also being used in restarting the

dynamics, it will automatically reset QLDM. Therefore, LDRS does not

need to be called in this case.

(d) LDERite

LDWRite provides specifications for writing out lambda dynamics, i.e.

the histogram of the lambda variables, the biasing potential etc. The

integer variable IUNLdm is the FORTRAN unit on which the output data

(unformatted) are to be saved. The value of the integer NSAVL sets step

frequency for writing lambda histograms. IUNLdm is defaulted to -1 and

NSAVL is defaulted to 0. Both IUNLdm and NSAVl can be reset in DYNAmics

command (Please refer to

the following script will set IUNLdm with unit No. 8 and NSAVL equal to 10:

LDWRite IUNL 8 NSAVL 10

(e) RMBOnd and RMANgle

Since each energy term is scaled by lambda, RMBOnd and RMANgle can prevent

bond breaking caused by such scaling during dynamic simulations. Alternatively

one can fix bonds (and angles) using SHAKE. But is is not always possible.

(f) MSLD

Multi-Site lambda-dynamics is a generalized version of the original

lambda-dynamics. Greater numerical stability of the simulations

is acheived with the MSLD definitions of lambda which implicitly

satisfy the constraints a) that each lambda value varies between 0 and 1 and

b) that the lambda values for a given Site sum to 1 (see the functional

forms listed above). Any system set up for the original lambda-dynamics

(i.e. that has multiple blocks at only one Site) can be run using MSLD.

In this case, the system would be set up in BLOCK as before, but the LDMA

command would be replaced by the MSLD commands.

For example, the original lambda-dynamics, using the theta-dynamics option

(qldm test) setup would be:

BLOCK 4

Call 2 sele site1sub1 end

Call 3 sele site1sub2 end

Call 4 sele site1sub3 end

qldm theta

lang temp 310.0

ldin 1 1.0 0.0 12.0 0.0 5.0

ldin 2 0.50 0.0 12.0 0.0 5.0

ldin 3 0.20 0.0 12.0 3.2 5.0

ldin 4 0.30 0.0 12.0 -1.0 5.0

rmla bond thet

ldma ! use for original lambda-dynamics

END

and the MSLD setup would be:

BLOCK 4

Call 2 sele site1sub1 end

Call 3 sele site1sub2 end

Call 4 sele site1sub3 end

qldm theta ! required for MSLD

lang temp 310.0

ldin 1 1.0 0.0 12.0 0.0 5.0

ldin 2 0.50 0.0 12.0 0.0 5.0

ldin 3 0.20 0.0 12.0 3.2 5.0

ldin 4 0.30 0.0 12.0 -1.0 5.0

rmla bond thet

msld 0 1 1 1 fnex 5.5 ! use for MSLD

msma ! use for MSLD

END

Lambda trajectory files written by MSLD can be analyzed by TRAJ LAMB

commands. The header contains all the information required to process

the trajectory (e.g. number of blocks, which blocks are assigned to

which site etc.). The lambda trajectory files are specified in the

DYNAMICS commands using keywords:

IUNLDM unit ! where unit corresponds to the unit number of the

lambda trajectory file

NSAVL freq ! where freq corresponds to the frequency of writing

the lambda values

The TRAJ LAMB command will process the lambda trajectory file and print

out statistics related to individual sites ("single-site" statistics):

* the population of each block (population = the number

of snapshots in which each block(i) has lambda(i) = 1, or more

specifically, the number of snapshots in which each block(i) has

lambda(i) > threshold).

* the number of transitions at each Site (i.e. the number of times

the identity of the block with lambda(i) > threshold changes).

* and the relative free energies for each pair of blocks at each Site.

(without and with the correction for the fixed lambda biased invoked in

the LDIN command)

Output is provided for two threshold values (default 0.8 and 0.9) for

approximating lambda(i) = 1 to provide an estimate of the sensitivity of

the results to the specific threshold used:

lambda(i) = 1, if lambda(i) > threshold

For systems with more than one site (i.e. sites at which multiple blocks

are modeled), a complete physical ligand is present at a given snapshot

when there is a block with lambda > threshold at each Site. For a given

system, there are a total of N(site_1) x N(site_2) x ... N(site_n)

possible ligands where N(i) is the number of blocks at Site i.

For systems with two sites, in addition to the general "single-site"

statistics, the TRAJ LAMB command will account for all combinations of

the blocks and print out "multi-site" statistics:

* the populations of each "ligand" for two thresholds (population =

the number of snapshots in which each "ligand" exists, i.e. the

combination of blocks corresponding to the ligand each have lambda = 1)

* the number of transitions between these ligands * the relative free

energies of each pair of ligands (without and with the correction for

the fixed lambda biased invoked in the LDIN command)

For systems with more than two sites, it is recommended that you use

the TRAJ LAMB PRINT command to print out the lambda values for each

snapshot and perform the population analysis and compute the relative

free energies yourself.

See TRAJ LAMB in dynamcs.info for a complete list of options.

E.g.:

To read header information only:

open unit 24 read file name scratch/msld_prod.lmd

traj lamb query unit 24

close unit 24

To process the trajectory file and print out lambda values at each

timestep:

open unit 24 read file name scratch/msld_prod.lmd

traj lamb print first 24 nunit 1

close unit 24

While the trajectory is being processed, the following internal variables are

stored:

'TMIN' - Minimum number of transitions for any site in the system

'TMAX' - Maximum number of transitions for any site in the system

'FPL' - Fraction of the snapshots which represent full Physical Ligands

'POP#' - Population for the substituent associated with indicated BLOCK number

at the low threshold value (e.g. the ?pop2 contains the population for

substituent in BLOCK 2 given CUTLO threshold)

'DDG#_#' - Relative free energy between the first and second substituents

listed at the low threshold value (e.g. ?ddg2_5 is the relative free energy

between the substituents associated with BLOCKS 2 and 5).

If for any reason you wish to suppress the storage of internal variables

(for example, if you have many substituents in your system and alreadyt

many internal variables have been stored such that processing the MSLD

trajectory gives a fatal error indicative of too many variables) then

include the keyword "nosub" in the trajectory command, i.e.:

open unit 24 read file name scratch/msld_prod.lmd

traj lamb print first 24 nunit 1 nosub

close unit 24

A warning is in order: the BLOCK module is quite user-unfriendly, AND

the user (=you) has to know what he/she is doing, otherwise you won't

get anywhere! (Of course, this could be a blessing in disguise) There

are two applications for BLOCK: (i) Mere use as an energy partitioning

facility, which may, e.g., very helpful as an alternative to the

INTEraction energy command and (ii) use in free energy simulations.

The focus here is on free energy applications. The following paragraphs

assume that you are familiar with the theory of free energy difference

simulations (e.g. Brooks et al. Advances in Chem. Physics, Vol. LXXI,

1988, chapter V); the emphasis here is to show how a rough tool as

BLOCK can be used to implement the theory in a program and (of course)

how to use it.

Using BLOCK in order to calculate a free energy difference consists

out of two rather dissimilar parts (as far as practical problems are

concerned): (i) Run your system at various values of lambda and save

trajectories. (ii) Postprocess the trajectories with the FREE or the

EAVG command (possibly COMP), use the quantities which these modules

give you to calculate the free energy difference.

(i) The actual simulations

==========================

It's probably easiest to use a concrete example, and the free energy

difference between ethane and methanol in aqueous solution is used for

that purpose. BLOCK is a so-called dual topology method (D. Pearlman,

JPC 1994, 98, 1487) i.e. one has to duplicate any atom that is

different with respect to any of its parameters. In the

ethane/methanol case this means that you have to run with a solute

which looks something like

H1

\ /H4

\ C1E ---- C2-H5

H2 = { } \H6

/ C1M --- OG

/ \HG1

H3

(and there is water.)

Conceptually, this system is divided into three regions:

environment: water, H1, H2, H3 (the region where nothing changes)

reactant: C1E, C2, H4, H5, H6 (ethane half)

product: C1M, OG, HG1 (methanol half),

where of course the role of reactant and product is interchangeable.

The steps involved to start running dynamics are as follows:

(1) set up the hybrid (generate psf). In principle straightforward,

but there is a practical pitfall: The autogenerate angles and

dihedrals option(s) may produce artificial dihedrals/angles between

the two/three parts of the system, e.g. you don't want angles

H1-C1E-OG etc. or dihedrals H3-C1M-C2-H4 etc. Also, make sure to

specify nonbonded exclusions between the reactant and product part,

otherwise you'll get endless distance warnings and may even bomb if

two atom positions coincide.

(2) Place the hybrid into water (stochastic or periodic boundary

conditions -- yes, IMAGE is now supported) as usual

(3) Partition the system, i.e. enter BLOCK

The following script fragment will do the trick:

block 3

call 2 sele <reactant> end

call 3 sele <product> end

end

(reactant and product have to be defined according to your system).

BLOCK 3 initializes the block module with 3 blocks, all atoms are in

block 1. The two CALL commands bring the reactant and product part of

the system into block 2 and 3 respectively.

(4) Run the necessary MD simulations. Let's assume that you decide to

use the following values of lambda, lambda = 0.1, 0.3, 0.5, 0.7, 0.9.

You want to start your simulation at lambda = 0.1 and you have already

partitioned your system as shown in (3). (This information is kept

within the same script between calls to block, but it is not saved in

restart files or the psf, i.e. you have to repeat this step (as well

as step (3)) in every input file). Enter block again, e.g.

block

lamb 0.1

end

From now on interactions between the 3 blocks will be scaled according

to the following matrix (lambda = l = 0.1 ==> 1-l = 0.9):

block | 1 2 3

------|--------------------

1 | 1.0 1-l l

2 | 1-l 1-l 0.

3 | l 0. l

Please note that BLOCK will first calculate an interaction, then check

to which block the two atoms belong and scale the energy (and forces)

appropriately. Therefore, if the distance between 2 atoms is zero

(e.g. in the ethane/methanol example I would define C1M and C1E on top

of each other!) then you need non-bonded exclusions, otherwise you

encounter a division by 0 error!

The LAMB command is a shortcut for the following sequence of COEF

commands, the following code fragment should be self-explanatory:

block

coef 1 1 1.0

coef 1 2 0.9

coef 1 3 0.1

coef 2 2 0.9

coef 2 3 0.0

coef 3 3 0.1

end

BLOCK only accepts and uses symmetric matrices, i.e. it doesn't

matter whether you specify COEF 1 2 or COEF 2 1.

Whenever you now call the energy routines, the energies/forces

returned from them will be scaled according to the matrix you have set

up. Minimizers and Dynamics can be used as always. So you are ready

to run dynamics, and for arguments sake say that you run at every

value of lambda 10,000 steps equilibration and 20,000 steps production

(i.e. you save coordinates to trajectories) You don't need to save

every step, every 5th to 20th step is probably more than enough. (If

you saved every step you'd obtain highly correlated data, i.e. you

have larger trajectories, but you won't gain anything in terms of

convergence.)

(ii) Post-processing -- how to obtain a free energy difference

==============================================================

At this point in our example, you would have five trajectories

corresponding to lambda = 0.1, 0.3, ..., 0.9 The BLOCK module now has

to be used to obtain the average quantities you need for either the

exponential formula (FREE) or thermodynamic integration (EAVG,COMP)

from the trajectories you generated in step (i)

(1) At this point, some issues regarding the non-bonded list have to

be considered. No special considerations were necessary while running

dynamics (aside from having some non-bonded exclusions where

necessary); you just set up list updates as usual. During

post-processing there are two considerations: (a) efficiency -- you

just want to calculate the necessary subset of interactions (otherwise

your post-processing run will take about as much time as the

simulation itself), and (b) proper list-updating.

(a) Efficiency: In none of the post-processing routines do you need

the interactions between particles that belong to the environment;

therefore you should avoid calculating them. This can be done easily

by specifying

cons fix sele <environment> end

Note that this is not necessary, but it will reduce the CPU time

necessary from hours to minutes (and results are identical!) However,

if you had atoms belonging to reactant or product or both FIXed during

the simulations in step (i), you MUST NOT FIX them now; otherwise

you'll omit contributions.

(b) List updating: While the efficiency considerations in principle

are optional, you have to follow one of the two strategies below

otherwise you'll get erroneous results. If you used IMAGE, you have

to use the second protocol! Originally, the BLOCK post-processing

commands would not do any list updating. This meant that you had to

have a nonbonded list which would include all possible interactions

before starting post-processing -- don't forget that you post-process

over, e.g., 20 ps and particles will move quite far. You can easily

create such a nonbonded list by specifying a CUTNB value of, e.g. 99.

or 999. Ang (surely, all possible interactions will be included). A

!set up system (psf, initial coordinates)

block

!partition system

end

cons fix sele <environment> end

==> energy cutnb 99. <all other options as during dynamics>

!open trajectories

block

!postprocessing

end

In this case, do not use the inbf, ihbf and imgf options of the

post-processing commands, they will default to 0, i.e. no update.

This approach, however, CANNOT work with IMAGES! Proper use of IMAGEs

requires that the minimum image convention is checked periodically,

i.e. particles have to be repartitioned between primary and image

region. As the BLOCK post-processing commands now understand INBF,

IHBF and IMGF, this doesn't pose a problem. However, the automated

update is not supported (if you specify a negative value, you'll get a

mild warning and the system will default to +1), and I recommend that

you use 1 for all frequencies (don't forget, the frames in your

trajectory are several steps apart, i.e. in general an update may be

necessary) The above scheme now looks like:

!set up system (psf, initial coordinates)

block

!partition system

end

cons fix sele <environment> end

! set up images if needed

==> energy <all options, incl. CUTNB, as during dynamics>

!open trajectories

block

eavg <other options> inbf 1 ihbf ? (imgf 1)

end

Unless you have explicit hbond terms, ihbf can of course be 0!

(Please note that there may or may not be problems with CRYSTAL, see

Limitations section)

(2) The actual post-processing commands. In the following I'll

explain how to set things up for FREE, EAVG and COMP (as well as why).

To speed up things further, you'll also want to specify the NOFOrce

option at some point.

FREE: This module allows you to calculate the necessary ensemble

average for the exponential formula. Using our example, you can for

example estimate the free energy difference between l=0.1 (a value at

which you ran a trajectory) and l=0.0, or, based on your l=0.1

trajectory the free energy difference between l=0.0 and 0.2 (double

wide sampling), i.e.

A(0.0)-A(0.1) = -k_B*T*ln <exp[-(U(l=0.0)-U(l=0.1))/kT]>_(l=0.1)

or

A(0.2)-A(0.0) = -k_B*T*ln <exp[-(U(l=0.2)-U(l=0.0))/kT]>_(l=0.1)

You should set up your system with 3 blocks and the usual environment,

reactant and product partitions. Before entering block to issue the

free command, you have to open the trajectory/ies.

! all the stuff shown above for non-bond lists

open file unit 10 read name dat01.trj

block

free oldl 0.1 newl 0.0 first 10 nunit 1 [temp 300. -

inbf 1 imgf 1]

end

or, for double wide sampling, the free line would be replaced by

free oldl 0.0 newl 0.2 first 10 nunit 1 [temp 300. -

inbf 1 imgf 1]

Here dat01.trj is the trajectory which contains your 20 ps of dynamics

at lambda = 0.1. Based on the oldl/newl values (which correspond to

A(newl) - A(oldl)), FREE generates the appropriate interaction matrix,

which it prints; I recommend that you try to understand why it

generates this matrix! FIRST is the unit number of the first

trajectory file (10 in our example), NUNIT is the number of

trajectories (1 in our example). These (and the other options

regarding the trajectories work as in any other post-processing

command in CHARMM, see e.g. the TRAJ command) The update frequencies

are optional depending on how you decided to handle your non-bonded

updates. temp defaults to T=300 K, cf. equations above.

If you specify CONT +n, you'll get a cumulative average every n steps;

in this case the last value equals the final result; if you specify CONT

-n, you'll get the average over every n frames, plus of course the

final result at the end.

Note that trajectories are not rewound after use; i.e. before any

subsequent FREE (or EAVG,COMP) command you have to rewind (or reopen)

them!

Once you have all the free energy pieces you need, you simply add them

up to obtain the free energy difference (beware of sign errors

depending on how you defined oldl/newl)

EAVG: The main use of this module lies in obtaining the required

ensemble averages for thermodynamic integration. The most significant

difference to EAVG is that you have to specify your own interactions

matrix. BLOCK uses linear coupling in lambda in the potential energy

function, i.e.

V(l) = V0 + (1-l)*V_reac + l*V_prod,

where V0 contains all the intra-environment terms, V_reac are the

intra-reactant and reactant-env. interactions, and V_prod are the

intra-product and product-env. interactions, respectively. The

quantity of interest in TI is dV/dl; for the above potential energy

function we have

dV/dl = V_prod - V_reac

It's very easy to obtain this quantity from EAVG. Use 3 blocks,

partition the system as before.

! all the stuff shown above for non-bond lists

open file unit 10 read name dat01.trj

block

coef 1 1 0.

coef 1 2 -1.

coef 2 2 -1.

coef 1 3 1.

coef 2 3 0.

coef 3 3 1.

eavg first 10 nunit 1 [inbf 1 imgf 1 cont +-n]

end

You will calculate the average interaction energy over all the frames

in the trajectory according to the following (symmetric) matrix

0.0

-1.0 -1.0

1.0 0.0 1.0;

i.e. it's easy to see that the above script will give you <V_prod -

V_reac>_(l=0.1). If you post-process the other trajectories (l=0.3,

0.5, ..,0.9) in an analogous fashion, you just have to approximate the

TI integral by the trapezoidal formula (for basic Newton Cotes

formulae (open and closed) see, e.g., Numerical Recipes), i.e. in this

case you would have

dA = 0.2 * (dV(0.1)+dV(0.3)+...+dV(0.9)),

where dV(0.1) = <V_prod - V_reac>_(l=0.1), etc.

The above is an example of the basic use of EAVG. You automatically

get the formal components according to interaction type. Cont +-n

works similarly to the FREE case. If you wanted to exclude the

intramolecular contributions from ethane and methanol you could set up

a slightly different coefficient matrix, i.e.

coef 1 1 0.

coef 1 2 -1.

coef 2 2 0.

coef 1 3 1.

coef 2 3 0.

coef 3 3 0.

and you'll get only the solute-solvent contributions. You can use

more blocks (m > 3) to extract only a subset of interactions, e.g.

block 1: environment - x

block 2: reactant

block 3: product

block 4: x,

where x is the region of interest, e.g. a specific sidechain in a

protein (but not the one that is mutated!)

Using EAVG with an appropriate coefficient matrix, e.g.

coef 1 1 0.

coef 1 2 0.

coef 1 3 0.

coef 1 4 0.

coef 2 2 0.

coef 2 3 0.

coef 2 4 -1.

coef 3 3 0.

coef 3 4 1.

coef 4 4 0.

will give you (after integration over lambda) the free energy

contribution of the interaction of sidechain x with the mutation site.

Note that such formal free energy components may be (strongly)

path-dependent. These last two examples have hopefully provided a

flavor of what can be done with the EAVG module.

COMP: This module is also used for thermodynamic integration. It

always operates with four (and only four) blocks, just as the advanced

example last given for EAVG, so it facilitates COMPonent analysis.

Here I want to focus on the second unique aspect of COMP, it's

capability to extrapolate additional datapoints, and so I consider in

the framework of our ethane/methanol example the "special" case where

I want the total free energy difference (as before in EAVG). In order

to do this, the system needs to be partitioned as follows

block 1: --

block 2: reactant

block 3: product

block 4: environment

Whereas EAVG gave us <V_prod - V_reac>_l only for those lambda values

at which we had actually done the simulations, COMP gives us

additional values via perturbation (see Bruce Tidor's thesis). Using

! all the stuff shown above for non-bond lists

open file unit 10 read name dat01.trj

block

coef 1 1 0.

coef 1 2 0.

coef 1 3 0.

coef 1 4 0.

coef 2 2 -1.

coef 2 3 0.

coef 2 4 -1.

coef 3 3 1.

coef 3 4 1.

coef 4 4 0.

comp first 10 nunit 1 [inbf 1 imgf 1] dell 0.06667 ndel 1

end

will now give us <V_prod - V_reac>_l at l=0.03334, l=0.1 and

l=0.16667. If we use the same script on the other trajectories, we

have 15 instead of 5 datapoints for the integration, i.e. we can

obtain dA as

dA = 0.06667 * (dV'(0.03334)+dV(0.1)+...+dV'(0.96667)),

where dV(0.1) = <V_prod - V_reac>_(l=0.1), etc. and the ' indicates

that this is a perturbed quantity. In principle, this

should give a better numerical integration; however, in practice

everything depends on how well your actual data (l=0.1, 0.3, ...,0.9)

are converged.

There is no check whether your ndel/dell combination is meaningful;

and you cannot run COMP without using the perturbation feature, i.e.

NDEL should be set to at least 1 (valid values are 1 through 5). The

defaults (if you don't specify ndel/dell) lead to an invalid input

(This should be fixed...)

(iii) Lambda-dynamics simulations

=================================

In an efforts to make the transition from using previous subcommands

to running the lambda dynamics as smoothly as possible, we purposely

parallel new syntax after the COEF subcommand. There are

total of eight new keywords for setting up new dynamics. They are

classified according to their functionality.

(a) LDINitialize and LDMAtrix

These two keywords are basic commands for starting the lambda

dynamics run. The correct use of them is tied together with the BLOCK

and CALL commands. Using the same example as the one given in "the

actual simulations", the input script fragment will be as following:

block 3

call 2 sele <reactant> end

call 3 sele <product> end

LDIN 1 1.0 0.0 20.0 0.0

LDIN 2 0.9 0.0 20.0 0.0

LDIN 3 0.1 0.0 20.0 0.0

LDMA

end

Here, the LDINitialize command models after the COEF command with

the format

LDIN INDEX LAMBDA**2 LAMBDAV LAMBDAM LAMBDAF

Several comments are in order. First, notice that [lambda(1)**2]

= 1.0 and [lambda(2)]**2 + [lambda(3)]**2 = 1.0. They are quite

similar to the inputs of COEF subcommand. However, since one

index instead of a pair is required here, only diagonal elements

of the interaction coefficient matrix are specified. To fill up

the matrix, LDMA is provided to finish the job automatically.

In general, if there is total of N blocks, the first one is

by default assumed to be the region where nothing changes.

Therefore, [lambda(1)**2] = 1.0 is always true. The condition

N

____

\

/ [lambda(i)**2] = 1.0 (1)

----

i = 2

has to be satisfied for the partion of the system Hamiltonian.

Due to some technical reasons in our implementation (details

see PDETAIL.DOC), we have used [lambda(i)**2] instead of lambda(i)

in our partion of the system Hamiltonian. Next, to make sure the above

condition is met at any given simulation step, we have also enforced a

condition containing velocities of the lambda variables

N

____

\

/ lambda(i)*lambdaV(i) = 0.0 (2)

----

i = 2

We used lambdaV(i) = 0.0 in the above script just to simplify the

input. As far as the mass parameter lambdaM is concerned, the minimum

requirement is that the value of mass has to be chosen such that the

time step (or frequency) of lambda variables is consistent with that

used for spatial coordinates x, y, z. Since the lambda variable is

introduced into the system by using extended Lagrangian,

considerations gone into the similar quantities, such as the

adjustable parameter Q in a Nose thermostat are applicable to the

choice of lambdaM. Some crude estimation can be made by examining

the derivative of the system Hamiltonian with respect to the

lambda, the curvature (simple harmonic approximation) or energy

difference between two end-point states (0 and 1). Our experience

has indicated that a conservative choice of the mass, i.e. a little

bit heavier mass than that of the crude estimate, serves us well

so far.

The biasing potential LAMBDAF has two functions: (1) In the screening

calculations LAMBDAF corresponds to the free energy difference of the

ligands in the unbound state. Such calculations can identify ligands

with favorable binding free energy and a ranking of the ligands can be

obtained from the probability of each ligand in the lambda=1 state;

(2) In precise free energy calculations, LAMBDAF corresponds to the best

estimate of free energy from previous calculations. Therefore the

estimate of free energy can be improved iteratively.

(b) LDBI and LDBV

In order to provide better control over simulation efficiency and

sampling space, an option of applying biasing (or umbrella)

potentials is furnished. LDBI specifies how many biasing

potentials will be applied and LDBV supplies all the details.

The general input format is

LDBV INDEX I J CLASS REF CFORCE NPOWER

Let us look at the following script

block

LDBI 3

LDBV 1 2 2 1 0.2 40.0 2

LDBV 2 3 3 2 0.6 50.0 2

LDBV 3 2 3 3 0.0 20.0 2

end

It states that there is total of 3 biasing potentials. The first one

(INDEX = 1) is acting on lambda(2) itself (I = J = 2), the second one

on lambda(3) and the third one is coupling lambda(2) and lambda(3)

together. At the moment, five different classes of functional forms

are supported:

CLASS 1:

__

| CFORCE*(lambda - REF)**NPOWER if lambda < REF

V =|

| 0 otherwise

|__

CLASS 2:

__

| CFORCE*(lambda - REF)**NPOWER if lambda > REF

V =|

| 0 otherwise

|__

CLASS 3:

V = CFORCE*[lambda(I) - lambda(J)]**NPOWER

CLASS 4:

__

| CFORCE*(1.0 - ((lambda - REF)**2)/REF**2) if lambda < REF

V =|

| 0 otherwise

|__

CLASS 5:

V = CFORCE*lambda(I)

note: the CLASS 5 biasing potential is the same as invoking the

biasing potential LAMBDAF in LDIN (except these biases will not

currently be taken into account in the TRAJ analysis routines).

CLASS 6:

V = CFORCE*[lambda(I) * lambda(J)]

CLASS 7:

V = CFORCE*[lambda(I) * (1 - lambda(I))]/[lambda(I) + REF]

CLASS 8:

V = CFORCE*[lambda(I) * lambda(J)]/[lambda(I) + REF]

CLASS 9:

V = CFORCE*[lambda(J) * (1 - ((lambda(I) + REF)/REF)**NPOWER)]

CLASS 10:

V = CFORCE*[lambda(J) * (1 - exp(REF*lambda(I)))]

(c) LDRStart

LDRStart is used only if for some reason, e.g. execution of EXIT command,

the logical variable QLDM for the lambda dynamics has been set to false.

In this case, to restart the dynamics, LDRStart can be used to reset

QLDM = .TRUE.. However, if LDIN is also being used in restarting the

dynamics, it will automatically reset QLDM. Therefore, LDRS does not

need to be called in this case.

(d) LDERite

LDWRite provides specifications for writing out lambda dynamics, i.e.

the histogram of the lambda variables, the biasing potential etc. The

integer variable IUNLdm is the FORTRAN unit on which the output data

(unformatted) are to be saved. The value of the integer NSAVL sets step

frequency for writing lambda histograms. IUNLdm is defaulted to -1 and

NSAVL is defaulted to 0. Both IUNLdm and NSAVl can be reset in DYNAmics

command (Please refer to

**»**dynamc for details).the following script will set IUNLdm with unit No. 8 and NSAVL equal to 10:

LDWRite IUNL 8 NSAVL 10

(e) RMBOnd and RMANgle

Since each energy term is scaled by lambda, RMBOnd and RMANgle can prevent

bond breaking caused by such scaling during dynamic simulations. Alternatively

one can fix bonds (and angles) using SHAKE. But is is not always possible.

(f) MSLD

Multi-Site lambda-dynamics is a generalized version of the original

lambda-dynamics. Greater numerical stability of the simulations

is acheived with the MSLD definitions of lambda which implicitly

satisfy the constraints a) that each lambda value varies between 0 and 1 and

b) that the lambda values for a given Site sum to 1 (see the functional

forms listed above). Any system set up for the original lambda-dynamics

(i.e. that has multiple blocks at only one Site) can be run using MSLD.

In this case, the system would be set up in BLOCK as before, but the LDMA

command would be replaced by the MSLD commands.

For example, the original lambda-dynamics, using the theta-dynamics option

(qldm test) setup would be:

BLOCK 4

Call 2 sele site1sub1 end

Call 3 sele site1sub2 end

Call 4 sele site1sub3 end

qldm theta

lang temp 310.0

ldin 1 1.0 0.0 12.0 0.0 5.0

ldin 2 0.50 0.0 12.0 0.0 5.0

ldin 3 0.20 0.0 12.0 3.2 5.0

ldin 4 0.30 0.0 12.0 -1.0 5.0

rmla bond thet

ldma ! use for original lambda-dynamics

END

and the MSLD setup would be:

BLOCK 4

Call 2 sele site1sub1 end

Call 3 sele site1sub2 end

Call 4 sele site1sub3 end

qldm theta ! required for MSLD

lang temp 310.0

ldin 1 1.0 0.0 12.0 0.0 5.0

ldin 2 0.50 0.0 12.0 0.0 5.0

ldin 3 0.20 0.0 12.0 3.2 5.0

ldin 4 0.30 0.0 12.0 -1.0 5.0

rmla bond thet

msld 0 1 1 1 fnex 5.5 ! use for MSLD

msma ! use for MSLD

END

Lambda trajectory files written by MSLD can be analyzed by TRAJ LAMB

commands. The header contains all the information required to process

the trajectory (e.g. number of blocks, which blocks are assigned to

which site etc.). The lambda trajectory files are specified in the

DYNAMICS commands using keywords:

IUNLDM unit ! where unit corresponds to the unit number of the

lambda trajectory file

NSAVL freq ! where freq corresponds to the frequency of writing

the lambda values

The TRAJ LAMB command will process the lambda trajectory file and print

out statistics related to individual sites ("single-site" statistics):

* the population of each block (population = the number

of snapshots in which each block(i) has lambda(i) = 1, or more

specifically, the number of snapshots in which each block(i) has

lambda(i) > threshold).

* the number of transitions at each Site (i.e. the number of times

the identity of the block with lambda(i) > threshold changes).

* and the relative free energies for each pair of blocks at each Site.

(without and with the correction for the fixed lambda biased invoked in

the LDIN command)

Output is provided for two threshold values (default 0.8 and 0.9) for

approximating lambda(i) = 1 to provide an estimate of the sensitivity of

the results to the specific threshold used:

lambda(i) = 1, if lambda(i) > threshold

For systems with more than one site (i.e. sites at which multiple blocks

are modeled), a complete physical ligand is present at a given snapshot

when there is a block with lambda > threshold at each Site. For a given

system, there are a total of N(site_1) x N(site_2) x ... N(site_n)

possible ligands where N(i) is the number of blocks at Site i.

For systems with two sites, in addition to the general "single-site"

statistics, the TRAJ LAMB command will account for all combinations of

the blocks and print out "multi-site" statistics:

* the populations of each "ligand" for two thresholds (population =

the number of snapshots in which each "ligand" exists, i.e. the

combination of blocks corresponding to the ligand each have lambda = 1)

* the number of transitions between these ligands * the relative free

energies of each pair of ligands (without and with the correction for

the fixed lambda biased invoked in the LDIN command)

For systems with more than two sites, it is recommended that you use

the TRAJ LAMB PRINT command to print out the lambda values for each

snapshot and perform the population analysis and compute the relative

free energies yourself.

See TRAJ LAMB in dynamcs.info for a complete list of options.

E.g.:

To read header information only:

open unit 24 read file name scratch/msld_prod.lmd

traj lamb query unit 24

close unit 24

To process the trajectory file and print out lambda values at each

timestep:

open unit 24 read file name scratch/msld_prod.lmd

traj lamb print first 24 nunit 1

close unit 24

While the trajectory is being processed, the following internal variables are

stored:

'TMIN' - Minimum number of transitions for any site in the system

'TMAX' - Maximum number of transitions for any site in the system

'FPL' - Fraction of the snapshots which represent full Physical Ligands

'POP#' - Population for the substituent associated with indicated BLOCK number

at the low threshold value (e.g. the ?pop2 contains the population for

substituent in BLOCK 2 given CUTLO threshold)

'DDG#_#' - Relative free energy between the first and second substituents

listed at the low threshold value (e.g. ?ddg2_5 is the relative free energy

between the substituents associated with BLOCKS 2 and 5).

If for any reason you wish to suppress the storage of internal variables

(for example, if you have many substituents in your system and alreadyt

many internal variables have been stored such that processing the MSLD

trajectory gives a fatal error indicative of too many variables) then

include the keyword "nosub" in the trajectory command, i.e.:

open unit 24 read file name scratch/msld_prod.lmd

traj lamb print first 24 nunit 1 nosub

close unit 24

Top

(1) Please be advised (again) that the AVERage command is unsupported,

and I would not be surprised if it does not work (anymore). Unless

someone who understands this module better than I do maintains it, I

recommend that we remove it.

(2) BLOCK now coexists with IMAGE "peacefully" and essentially

transperantly to the user. It works correctly for the case of a

periodic water-box (cf. the block3.inp testcase). I would, however,

check carefully whether things really work before I would use it on

something fancier like infinite alpha helices. Similarly, it is not

clear to me whether things work with the CRYSTAL facility. If one

modifies block3 as to use CRYSTAL instead of IMAGE things (seem to)

work. On the other hand, I know that I didn't support XTLFRQ in the

post-processing routines as I don't understand its meaning. I'll fix

things if someone is willing to help me with the bits and pieces I

don't understand.

(3) Bond and bond angle terms (including Urey-Bradleys). Be advised

that if you run a simulation at lambda = 0 or lambda = 1 you may

effectively remove bond (and bond angle terms) as they get scaled by

zero. In other words, you would have ghost particles that can move

freely through your systems, and this leads to all sorts of nasty

side-effects. Furthermore, this approach is not sound theoretically

(S. Boresch & M. Karplus, unpublished). So in general, avoid running

at lambda = 0 and 1. If you have your bonds constrained you're safe

as the constraint will keep things together (that won't take care of

angles however!) In order to avoid artifacts from noisy, diverging

bond and bond angle contributions throw them out during

post-processing, e.g. by using the SKIP BOND ANGL UREY command before

starting block post-processing. If you want to see what can go wrong,

look at the block2 test-case...

" Dual Topology Soft Core Potential"

The new commands PSSP/NOPSsp and the optional parameters ALAM and

DLAM control the interactions between soft core potentials and BLOCK,

which is essentially the same as the PSSP command in the PERT soft

core (» pert ). After you specify PSSP inside BLOCK, soft core

LJ and electrostatic interactions will be used inside block interactions.

For the atom based NBOND command (NBOND ATOM), the block coefficents

(lambda) of VDW and ELEC can be defined as the different values. For

the group based case (NBOND GROUP), they share the same lambda value

currently. The separation parameters for elec. and LJ interactions can

be set with the ALAM and DLAM options, the default of 5A^2 should be

reasonable. The option is memorized, i.e., after the first invocation

of PSSP, all further calls of EVDW will use soft core interactions.

To turn this off, please use the NOPSsp keyword inside BLOCK/END pair.

NB! Requires FAST OFF and nonbond options SHIFT VSWITCH." -- New by H. Li and W. Yang

"Multisite lambda Dynamics Soft Core Potential"

The SOFT directive turns soft cores a la Hayes et al JPC B (2017) on or

off. These soft cores are intended for use with multisite lambda dynamics

and domdec. Outside of domdec, the standard hard cores are used. OFF turns

soft cores off, ON turns them on for nonbonded interactions, W14 turns them

on for nonbonded and 1-4 interactions.

"CHARMM/OpenMM Soft Core Potential"

The SOMM directive turns on the CHARMM/OpenMM soft cores ONLY for the vdW interactions

a la Hayes et al JPC B (2017). To be used in running TI with BLOCK through the CHARMM/OpenMM

interface, where the energies, forces and dynamics are integrated through OpenMM for

post analysis of the trajectory to use TI, FEP or MBAR (preferred).

"Multisite lambda Dynamics PME Electrostatics"

The PMEL directive controls how MSLD treats long range electrostatics with

PME. The PME potential is modified slightly, as described in Huang, Chen,

Wallace, and Shen, JCTC (2016). PMEL is only compatible with domdec. To use

PME with MLSD, PMEL must be invoked inside the block directive, but PME must

also be invoked as described in ewald.info and domdec.info by appropriately

setting the nonbonded options and domdec options.

PMEL OFF does not use PME electrostatics. PMEL ON scales all charges by the

lambda of their particular block in the k-space and self energy terms

(energy terms EWKS and EWSE). PME exclusions (energy term EWEX) are scaled

by the product of lambdas for substituents at different sites, by zero for

different substituents at the same site, and by lambda for intrasubstituent

or substituent-environment interactions. PMEL EX scales all charges by

lambda just like PMEL ON, but the exclusions are treated differently:

specifically, since intrasubstituent interactions are scaled by lambda

squared in the k-space term, they are also scaled by lambda squared in the

exclusions term. All other exclusion scaling remains the same. PMEL NN

scales exclusions by the product of the two lambdas regardless.

"Saving lambda Forces"

In order to write effective test cases and charmm scripts, sometimes it is

necessary to be able to examine the forces on lambda. "FLAM string int"

saves the lambda force for the block specified by int to the CHARMM

parameter whose name is given in string, much like the set command (see

by name using @ like any other CHARMM parameter.

"Scaling Bonded Interactions of Constrained Atoms"

Sometimes when converting between two closely related scaffolds with MSLD

it is desirable to convert the atom in one substituent directly to the

analagous atom in the other substituent, especially if the changing atoms

are in the core of th molecule rather than on the periphery. Reasons

include avoiding exploring larger conformational spaces in the off state

and avoiding double counting of all the bonded interactions which can

result in errors due to differing strain in the two halves of the

thermodynamic cycle. While direct conversion of the atoms is not offered

by the BLOCK module, it is possible to effectively convert them by

constraining their positions to overlap (for example with CONS NOE), and

then scaling their bonded interactions (bond, angle, dihe, impr, etc...)

by lambda. The primary reason for not scaling bonded interactions with

the RMLA directive is to prevent the atoms from drifting of and exploring

large conformational spaces, so if they are localized in some manner,

scaling their interactions no longer causes poor sampling and avoids

artifacts mentioned by Liu, Wang, and Mobley in Journal of Chemical

Information and Modeling 55:727-735 (2015)

SCAT ON enables Scaling of Constrained AToms (SCAT). SCAT OFF turns them

back off. SCAT K [real] sets the spring force constant that restrains each

atom to the center of mass. (Yes, they are technically restraints, not

constraints.) You can also set K to zero and use restraints from the CONS

module. Scaling of constrained atoms is only tested within domdec. Once

scaling has been turned on, each group of constrained atoms may be

specified with "CATS atom-selection". Any bonded interaction which would

normally be unscaled due to RMLA will be scaled by lambda if all atoms are

constrained or are part of the environment or another block. If any of the

atoms are unconstrained, the scaling of the interaction is dictated by

RMLA.

"Soft Bonds"

Sometimes it is necessary to break a bond in an alchemical transformation,

e.g. when running simulations that involve core swaps or macrocycles, or

other perturbations that change the topology of the core. Soft bonds are

currently only implemented in domdec.

NSOB int [RALF real] [LEXP real] [BLEX real] turns on soft bonds if int is

greater than 0, and turns them off otherwise. The integer gives the number

of soft bonds that will be allocated. RALF is the saturation radius of all

soft bonds in angstroms and defaults to 1. See JCTC 13:6290-6300 (2017)

for the functional form, their "alpha"=RALF^-2. Set RALF to a negative

value to get a "hard" bond with RALF=infinity. LEXP is the exponent

applied to the lambda scaling, and also defaults to 1. All other bonded

interactions including angles and dihedrals which include both atoms of

the soft bond will also be scaled by lambda^LEXP, but currently maintain

their "hard" functional form, including the singularities in the forces.

This fact can be exploited to scale interactions for a particular ijk

angle by lambda^LEXP by declaring a soft bond between i and k even though

they are not bonded. If a different lambda scaling exponent is desired for

the bonds and ureys relative to the angles, dihedrals, and impropers,

BLEX may be used to specify the former while LEXP will apply to the

latter, otherwise LEXP will apply to both.

Once the number of soft bonds has been declared, individual soft bonds are

specified with "SOBO int atom-selection1 atom-selection2" where int is the

index of the soft bond from 1 to NSOB, and the two selections specify the

two atoms in the soft bond.

Sometimes, especially when running dynamics with FFIX, it may be desirable to

start a simulation with a new lambda value from a restart file with an old

lambda value. To do this, set "RLFR OFF" (Read Lambda From Restart),

otherwise, CHARMM will read lambda and theta from the restart file.

"Adaptive Integration (ADIN) Method for Hybrid MD/MC Simulation"

In order to overcome the trapped distribution at certain lambda value in the

chemical space hybrid MD/MC simulation, adaptive integration method was

implemented. In this method, the biasing free energy potential is derived

by linearly integrating the ensemble average of energy derivatives at various

lambda values. By adaptive integration method, free energy difference between

two end states can be quickly computed. It is noted that this technique works

well when free energy has linear relationship with lambda value. It can crash

when there is severe end point singularity problem. Its general efficiency is

lower than the simulated scaling method, which does not suffer from end point

singularity problems. - by Lianqing Zheng and Wei Yang

"Theta-dynamics"

This is an alternative method for the original lambda-dynamics. Lambda**2 is

replaced by sin(theta)**2 and (1-lambda**2) by cos(theta)**2. Theta, instead

of lambda, now is the variable for propagation. This implementation can avoid

the artifacts brought in by the constant external works in the Lagarangian

Multiplier boundary treatment. In the theta-dynamics, history dependent

approaches can work very nicely with no danger of being trapped at the end

points. - by Lianqing Zheng and Wei Yang

"Multi-Site lambda-dynamics" (MSLD)

This is a more generalized lambda-dynamics method that allows

multiple substituents on multiple Sites on a common framework to be

evaluated simultaneously. Different functional forms of lambda have been

implemented which inherently satisfy the constraints that each lambda

should vary between 0 and 1 and the sum of the lambda values at a given

Site must equal 1. This strategy reduces the need to use Lagrangian

Multipliers and renormalization schemes and, for most systems, the timestep

can be increased in dynamics to 2 fs when SHAKE is invoked.

- by Jennifer L. Knight and Charles L. Brooks III

(1) Please be advised (again) that the AVERage command is unsupported,

and I would not be surprised if it does not work (anymore). Unless

someone who understands this module better than I do maintains it, I

recommend that we remove it.

(2) BLOCK now coexists with IMAGE "peacefully" and essentially

transperantly to the user. It works correctly for the case of a

periodic water-box (cf. the block3.inp testcase). I would, however,

check carefully whether things really work before I would use it on

something fancier like infinite alpha helices. Similarly, it is not

clear to me whether things work with the CRYSTAL facility. If one

modifies block3 as to use CRYSTAL instead of IMAGE things (seem to)

work. On the other hand, I know that I didn't support XTLFRQ in the

post-processing routines as I don't understand its meaning. I'll fix

things if someone is willing to help me with the bits and pieces I

don't understand.

(3) Bond and bond angle terms (including Urey-Bradleys). Be advised

that if you run a simulation at lambda = 0 or lambda = 1 you may

effectively remove bond (and bond angle terms) as they get scaled by

zero. In other words, you would have ghost particles that can move

freely through your systems, and this leads to all sorts of nasty

side-effects. Furthermore, this approach is not sound theoretically

(S. Boresch & M. Karplus, unpublished). So in general, avoid running

at lambda = 0 and 1. If you have your bonds constrained you're safe

as the constraint will keep things together (that won't take care of

angles however!) In order to avoid artifacts from noisy, diverging

bond and bond angle contributions throw them out during

post-processing, e.g. by using the SKIP BOND ANGL UREY command before

starting block post-processing. If you want to see what can go wrong,

look at the block2 test-case...

" Dual Topology Soft Core Potential"

The new commands PSSP/NOPSsp and the optional parameters ALAM and

DLAM control the interactions between soft core potentials and BLOCK,

which is essentially the same as the PSSP command in the PERT soft

core (» pert ). After you specify PSSP inside BLOCK, soft core

LJ and electrostatic interactions will be used inside block interactions.

For the atom based NBOND command (NBOND ATOM), the block coefficents

(lambda) of VDW and ELEC can be defined as the different values. For

the group based case (NBOND GROUP), they share the same lambda value

currently. The separation parameters for elec. and LJ interactions can

be set with the ALAM and DLAM options, the default of 5A^2 should be

reasonable. The option is memorized, i.e., after the first invocation

of PSSP, all further calls of EVDW will use soft core interactions.

To turn this off, please use the NOPSsp keyword inside BLOCK/END pair.

NB! Requires FAST OFF and nonbond options SHIFT VSWITCH." -- New by H. Li and W. Yang

"Multisite lambda Dynamics Soft Core Potential"

The SOFT directive turns soft cores a la Hayes et al JPC B (2017) on or

off. These soft cores are intended for use with multisite lambda dynamics

and domdec. Outside of domdec, the standard hard cores are used. OFF turns

soft cores off, ON turns them on for nonbonded interactions, W14 turns them

on for nonbonded and 1-4 interactions.

"CHARMM/OpenMM Soft Core Potential"

The SOMM directive turns on the CHARMM/OpenMM soft cores ONLY for the vdW interactions

a la Hayes et al JPC B (2017). To be used in running TI with BLOCK through the CHARMM/OpenMM

interface, where the energies, forces and dynamics are integrated through OpenMM for

post analysis of the trajectory to use TI, FEP or MBAR (preferred).

"Multisite lambda Dynamics PME Electrostatics"

The PMEL directive controls how MSLD treats long range electrostatics with

PME. The PME potential is modified slightly, as described in Huang, Chen,

Wallace, and Shen, JCTC (2016). PMEL is only compatible with domdec. To use

PME with MLSD, PMEL must be invoked inside the block directive, but PME must

also be invoked as described in ewald.info and domdec.info by appropriately

setting the nonbonded options and domdec options.

PMEL OFF does not use PME electrostatics. PMEL ON scales all charges by the

lambda of their particular block in the k-space and self energy terms

(energy terms EWKS and EWSE). PME exclusions (energy term EWEX) are scaled

by the product of lambdas for substituents at different sites, by zero for

different substituents at the same site, and by lambda for intrasubstituent

or substituent-environment interactions. PMEL EX scales all charges by

lambda just like PMEL ON, but the exclusions are treated differently:

specifically, since intrasubstituent interactions are scaled by lambda

squared in the k-space term, they are also scaled by lambda squared in the

exclusions term. All other exclusion scaling remains the same. PMEL NN

scales exclusions by the product of the two lambdas regardless.

"Saving lambda Forces"

In order to write effective test cases and charmm scripts, sometimes it is

necessary to be able to examine the forces on lambda. "FLAM string int"

saves the lambda force for the block specified by int to the CHARMM

parameter whose name is given in string, much like the set command (see

**»**miscom ). That lambda force can then be accessedby name using @ like any other CHARMM parameter.

"Scaling Bonded Interactions of Constrained Atoms"

Sometimes when converting between two closely related scaffolds with MSLD

it is desirable to convert the atom in one substituent directly to the

analagous atom in the other substituent, especially if the changing atoms

are in the core of th molecule rather than on the periphery. Reasons

include avoiding exploring larger conformational spaces in the off state

and avoiding double counting of all the bonded interactions which can

result in errors due to differing strain in the two halves of the

thermodynamic cycle. While direct conversion of the atoms is not offered

by the BLOCK module, it is possible to effectively convert them by

constraining their positions to overlap (for example with CONS NOE), and

then scaling their bonded interactions (bond, angle, dihe, impr, etc...)

by lambda. The primary reason for not scaling bonded interactions with

the RMLA directive is to prevent the atoms from drifting of and exploring

large conformational spaces, so if they are localized in some manner,

scaling their interactions no longer causes poor sampling and avoids

artifacts mentioned by Liu, Wang, and Mobley in Journal of Chemical

Information and Modeling 55:727-735 (2015)

SCAT ON enables Scaling of Constrained AToms (SCAT). SCAT OFF turns them

back off. SCAT K [real] sets the spring force constant that restrains each

atom to the center of mass. (Yes, they are technically restraints, not

constraints.) You can also set K to zero and use restraints from the CONS

module. Scaling of constrained atoms is only tested within domdec. Once

scaling has been turned on, each group of constrained atoms may be

specified with "CATS atom-selection". Any bonded interaction which would

normally be unscaled due to RMLA will be scaled by lambda if all atoms are

constrained or are part of the environment or another block. If any of the

atoms are unconstrained, the scaling of the interaction is dictated by

RMLA.

"Soft Bonds"

Sometimes it is necessary to break a bond in an alchemical transformation,

e.g. when running simulations that involve core swaps or macrocycles, or

other perturbations that change the topology of the core. Soft bonds are

currently only implemented in domdec.

NSOB int [RALF real] [LEXP real] [BLEX real] turns on soft bonds if int is

greater than 0, and turns them off otherwise. The integer gives the number

of soft bonds that will be allocated. RALF is the saturation radius of all

soft bonds in angstroms and defaults to 1. See JCTC 13:6290-6300 (2017)

for the functional form, their "alpha"=RALF^-2. Set RALF to a negative

value to get a "hard" bond with RALF=infinity. LEXP is the exponent

applied to the lambda scaling, and also defaults to 1. All other bonded

interactions including angles and dihedrals which include both atoms of

the soft bond will also be scaled by lambda^LEXP, but currently maintain

their "hard" functional form, including the singularities in the forces.

This fact can be exploited to scale interactions for a particular ijk

angle by lambda^LEXP by declaring a soft bond between i and k even though

they are not bonded. If a different lambda scaling exponent is desired for

the bonds and ureys relative to the angles, dihedrals, and impropers,

BLEX may be used to specify the former while LEXP will apply to the

latter, otherwise LEXP will apply to both.

Once the number of soft bonds has been declared, individual soft bonds are

specified with "SOBO int atom-selection1 atom-selection2" where int is the

index of the soft bond from 1 to NSOB, and the two selections specify the

two atoms in the soft bond.

Sometimes, especially when running dynamics with FFIX, it may be desirable to

start a simulation with a new lambda value from a restart file with an old

lambda value. To do this, set "RLFR OFF" (Read Lambda From Restart),

otherwise, CHARMM will read lambda and theta from the restart file.

"Adaptive Integration (ADIN) Method for Hybrid MD/MC Simulation"

In order to overcome the trapped distribution at certain lambda value in the

chemical space hybrid MD/MC simulation, adaptive integration method was

implemented. In this method, the biasing free energy potential is derived

by linearly integrating the ensemble average of energy derivatives at various

lambda values. By adaptive integration method, free energy difference between

two end states can be quickly computed. It is noted that this technique works

well when free energy has linear relationship with lambda value. It can crash

when there is severe end point singularity problem. Its general efficiency is

lower than the simulated scaling method, which does not suffer from end point

singularity problems. - by Lianqing Zheng and Wei Yang

"Theta-dynamics"

This is an alternative method for the original lambda-dynamics. Lambda**2 is

replaced by sin(theta)**2 and (1-lambda**2) by cos(theta)**2. Theta, instead

of lambda, now is the variable for propagation. This implementation can avoid

the artifacts brought in by the constant external works in the Lagarangian

Multiplier boundary treatment. In the theta-dynamics, history dependent

approaches can work very nicely with no danger of being trapped at the end

points. - by Lianqing Zheng and Wei Yang

"Multi-Site lambda-dynamics" (MSLD)

This is a more generalized lambda-dynamics method that allows

multiple substituents on multiple Sites on a common framework to be

evaluated simultaneously. Different functional forms of lambda have been

implemented which inherently satisfy the constraints that each lambda

should vary between 0 and 1 and the sum of the lambda values at a given

Site must equal 1. This strategy reduces the need to use Lagrangian

Multipliers and renormalization schemes and, for most systems, the timestep

can be increased in dynamics to 2 fs when SHAKE is invoked.

- by Jennifer L. Knight and Charles L. Brooks III

Top

Here is an example of independently scaling the attractive

and repulsive terms in the Lennard-Jones interaction:

! scale the interaction parameters

block 2

call 2 sele segid heli end

coeff 1 1 0.0 ! turn off the interactions between atoms in set 1

coeff 1 2 1.0 vdwa 0 vdwr 1.0 ! scaling ratio to scale interactions

! between protein and other atoms

coeff 2 2 1.0 ! leave interactions within the protein unchanged

end

In this example we turn off the attractive term (vdwa) in the LJ interaction

and have only hard-core repulsion.

Here is an example of independently scaling the attractive

and repulsive terms in the Lennard-Jones interaction:

! scale the interaction parameters

block 2

call 2 sele segid heli end

coeff 1 1 0.0 ! turn off the interactions between atoms in set 1

coeff 1 2 1.0 vdwa 0 vdwr 1.0 ! scaling ratio to scale interactions

! between protein and other atoms

coeff 2 2 1.0 ! leave interactions within the protein unchanged

end

In this example we turn off the attractive term (vdwa) in the LJ interaction

and have only hard-core repulsion.