# dynamc (c42b1)

Dynamics: Description and Discussion

There are four separate dynamics integrators available in CHARMM:

(This discussion does not apply to multi-body dynamics, which has a

separate set of integrators).

Name Keyword Module

Original Verlet ORIG dynamcv.src

Leapfrog Verlet LEAP dynamc.src (default)

Velocity Verlet VVER dynamvv.src

4-D L-F Verlet VER4 dynam4.src

New vel. Verlet VV2 dynamvv2.src

All methods are based on the Verlet scheme, and when used without

any special features, provide identical trajectories for short

simulations. All methods allow SHAKE.

The ORIG integrator is a standard 3-step Verlet integrator

with few frills. It allows:

Langevin Dynamics (LANG)

Thermodynamic Simulation Method (TSM)

The LEAP integrator is similar to the ORIG integrator, but does

provide increased accuracy (esp. for single precision version of

Langevin dynamics (LANG) (with accurate temperatures printed)

Constant Temperature and Pressure (CPT) (based on Berendsen's method)

Accurate pressures with SHAKE

High frequency correction to the total energy

Parallel code

Free energy equilibration indicator (deltaF*V) (with PERT)

Thermodynamic Simulation Method (TSM)

The VVER integrator also provides increase accuracy. It allows:

Constant Temperature (NOSE) (Nose-Hoover method)

Multiple Time Step (MTS)

The VER4 integrator enables the energy embedding technique that entails

placing a molecule into a higher spatial dimension [Crippen, G. M. &

Havel,T.F. (1990) J.Chem.Inf.Comput.Sci. Vol 30, 222-227].

The possibility of surmounting energy barriers with these added

degrees of freedom may lead to lower energy minima. Here, this is

accomplished by molecular dynamics in four dimensions. Specifically,

another cartesian coordinates was added to the usual X, Y, and Z

coordinates in the LEAPfrog VERLet algorithm.

The VV2 is a velocity-Verlet integrator based on the

operator-splitting technique. It works in conjunction with the

TPCONTROL command. It allows temperature and pressure control

[G. J. Martyna, M. E. Tuckerman, D. J. Tobias and M. L. Klein,

Mol. Phys. 87, 1117 (1996)], and provides an efficient

integration algorithm for polarizable force fields based on

Drude oscillators [G. Lamoureux and B. Roux, J. Chem. Phys. 119,

??? (2003)]. It uses a separate "SHAKE" algorithm, called

RATTLE/Roll.

In order to generate a dynamics trajectory, all requirements

for evaluating the energy must be met.

* Syntax | Syntax of the dynamics command

* Description | Description of the keywords and options

* Recommended | Recommended input options and values

* Discussion | Running dynamics

* Output | Output from a dynamics run

* Trajectory | Trajectory manipulation and I/O

* Merge | Merging or breaking up trajectory files into

different size pieces. Resampling at a larger

interval. Least squares fit to a reference.

Recentering, or undoing image operations.

* Reorient | Reorienting a coordinate trajectory

* RMSDyn | Computes the RMS difference between two trajectories

* Format | formatting and unformatting a dynamics trajectory

* CVELocity | Constant velocity dynamics

* TSALlis | Molecular dynamics in the Tsallis ensemble

* CENT | The reCENTering command

* CPT dynamics:» chmdoc/pressure . CPT dynamics

* 4-D dynamics:» chmdoc/fourd . 4-D dynamics

There are four separate dynamics integrators available in CHARMM:

(This discussion does not apply to multi-body dynamics, which has a

separate set of integrators).

**»**mbond .Name Keyword Module

Original Verlet ORIG dynamcv.src

Leapfrog Verlet LEAP dynamc.src (default)

Velocity Verlet VVER dynamvv.src

4-D L-F Verlet VER4 dynam4.src

New vel. Verlet VV2 dynamvv2.src

All methods are based on the Verlet scheme, and when used without

any special features, provide identical trajectories for short

simulations. All methods allow SHAKE.

The ORIG integrator is a standard 3-step Verlet integrator

with few frills. It allows:

Langevin Dynamics (LANG)

Thermodynamic Simulation Method (TSM)

The LEAP integrator is similar to the ORIG integrator, but does

provide increased accuracy (esp. for single precision version of

Langevin dynamics (LANG) (with accurate temperatures printed)

Constant Temperature and Pressure (CPT) (based on Berendsen's method)

Accurate pressures with SHAKE

High frequency correction to the total energy

Parallel code

Free energy equilibration indicator (deltaF*V) (with PERT)

Thermodynamic Simulation Method (TSM)

The VVER integrator also provides increase accuracy. It allows:

Constant Temperature (NOSE) (Nose-Hoover method)

Multiple Time Step (MTS)

The VER4 integrator enables the energy embedding technique that entails

placing a molecule into a higher spatial dimension [Crippen, G. M. &

Havel,T.F. (1990) J.Chem.Inf.Comput.Sci. Vol 30, 222-227].

The possibility of surmounting energy barriers with these added

degrees of freedom may lead to lower energy minima. Here, this is

accomplished by molecular dynamics in four dimensions. Specifically,

another cartesian coordinates was added to the usual X, Y, and Z

coordinates in the LEAPfrog VERLet algorithm.

The VV2 is a velocity-Verlet integrator based on the

operator-splitting technique. It works in conjunction with the

TPCONTROL command. It allows temperature and pressure control

[G. J. Martyna, M. E. Tuckerman, D. J. Tobias and M. L. Klein,

Mol. Phys. 87, 1117 (1996)], and provides an efficient

integration algorithm for polarizable force fields based on

Drude oscillators [G. Lamoureux and B. Roux, J. Chem. Phys. 119,

??? (2003)]. It uses a separate "SHAKE" algorithm, called

RATTLE/Roll.

**»**tpcontrol Dynamics.In order to generate a dynamics trajectory, all requirements

for evaluating the energy must be met.

**»**energy Needs.* Syntax | Syntax of the dynamics command

* Description | Description of the keywords and options

* Recommended | Recommended input options and values

* Discussion | Running dynamics

* Output | Output from a dynamics run

* Trajectory | Trajectory manipulation and I/O

* Merge | Merging or breaking up trajectory files into

different size pieces. Resampling at a larger

interval. Least squares fit to a reference.

Recentering, or undoing image operations.

* Reorient | Reorienting a coordinate trajectory

* RMSDyn | Computes the RMS difference between two trajectories

* Format | formatting and unformatting a dynamics trajectory

* CVELocity | Constant velocity dynamics

* TSALlis | Molecular dynamics in the Tsallis ensemble

* CENT | The reCENTering command

**»**monitor Monitor dihedral transitions* CPT dynamics:» chmdoc/pressure . CPT dynamics

**»**sgld Self-guided molecular/Langevin dynamics* 4-D dynamics:» chmdoc/fourd . 4-D dynamics

**»**pressure ressure. The pressure command**»**mts Multiple Time Scales Method**»**nose Nose-Hoover Dynamics**»**mbond ynamic. Multi-body DynamicsTop

Syntax for the Dynamics Command

DYNAmics { [ LEAP ] [ VERLet ] } ! Dynamics with the

{ [ NEW ] [ LANGevin ] } ! leap-frog integrator

{ [ CPT ] [ NOLAngevin] }

{ [ EULEr ] } [sgmd-sgld-spec] [cpt-spec] other-specs

{ [OMM] } [openmm-spec] !dynamics w/ openmm gpu module

{ ORIG } ! Dynamics with the verlet integrator

DYNAmics { VVERlet [ NOSE ] } ! Dynamics with the velocity verlet integrator

{ } other-specs

DYNAmics { LEAPfrog VER4 four-dim-spec } ! Four dimensional dynamics

{ } other-specs

DYNAmics { VV2 } [sgmd-sgld-spec] other-specs

DYNAmics { MBONd mbond-spec } other-specs ! Multibody dynamics

other-specs::= [NSTEp integer] [nonbond-spec] [hbond-spec] [frequency-spec]

{[TIMEstp real]} {STARt } [unit-spec] [temperature-spec] [options-spec]

{ AKMA real } {RESTart} [VSENd]

hbond-spec::=

nonbond-spec::=

mbond-spec::=

sgmd-sgld-spec::=

domdec-spec::=

openmm-spec::=

frequency-spec::= [INBFrq integer] [IEQFrq integer] [IHBFrq integer]

[IHTFrq integer] [IPRFrq integer] [NPRInt integer]

[NSAVC integer] [NSAVV integer] [NTRFrq integer]

[ILBFrq integer] [ISVFRQ integer] [NSAVL integer]

[IMGFrq integer] [IXTFrq integer]

[NLAT integer] [NSAVQ]

[NBLCkfep integer] [NSAVXyz integer] [MXYZ integer]

unit-spec::= [IUNCrd integer] [IUNRea integer] [IUNVel integer]

[IUNWri integer] [KUNIt integer] [CRAShu integer]

[BACKup integer] [IUNLdm integer] [IUNQ integer]

[ILAT integer] [IUNXyz integer]

[IBLCkfep integer]

[ILAP integer] [ILAF integer]

temperature-spec::= [FINAlt real] [FIRStt real] [TEMInc real]

[TSTRuc real] [TWINDH real] [TWINDL real]

[TBATh real]

options-spec::= [IASOrs integer] [IASVel integer] [ICHEcw integer]

[ISCAle integer] [ISCVel integer] [ISEEd repeat(integer)]

[SCALe real] [NDEGg integer] [RBUFfer real]

[AVERage] [ECHEck real] [TOL real]

cpt-spec::=

four-dim-spec::= [FIL4dimension] [SKBOnd] [SKANgle]

[SKDIhedral] [SKVDerWaals] [SKELectrostatics]

[K4DInitial real] [INC4Dforce integer]

[DEC4Dforce integer] [MULTK4di real]

[E4FILLcoordinates real]

[FNLT4 real] [FSTT4 real] [TIN4 real]

[IHT4 integer] [IEQ4 integer] [ICH4 integer]

[TWH4 real] [TWL4 real]

Syntax for the Dynamics Command

DYNAmics { [ LEAP ] [ VERLet ] } ! Dynamics with the

{ [ NEW ] [ LANGevin ] } ! leap-frog integrator

{ [ CPT ] [ NOLAngevin] }

{ [ EULEr ] } [sgmd-sgld-spec] [cpt-spec] other-specs

{ [OMM] } [openmm-spec] !dynamics w/ openmm gpu module

{ ORIG } ! Dynamics with the verlet integrator

DYNAmics { VVERlet [ NOSE ] } ! Dynamics with the velocity verlet integrator

{ } other-specs

DYNAmics { LEAPfrog VER4 four-dim-spec } ! Four dimensional dynamics

{ } other-specs

DYNAmics { VV2 } [sgmd-sgld-spec] other-specs

DYNAmics { MBONd mbond-spec } other-specs ! Multibody dynamics

other-specs::= [NSTEp integer] [nonbond-spec] [hbond-spec] [frequency-spec]

{[TIMEstp real]} {STARt } [unit-spec] [temperature-spec] [options-spec]

{ AKMA real } {RESTart} [VSENd]

hbond-spec::=

**»**hbonds .nonbond-spec::=

**»**nbonds .mbond-spec::=

**»**mbond DynDesc.sgmd-sgld-spec::=

**»**sgld .domdec-spec::=

**»**domdec .openmm-spec::=

**»**openmm .frequency-spec::= [INBFrq integer] [IEQFrq integer] [IHBFrq integer]

[IHTFrq integer] [IPRFrq integer] [NPRInt integer]

[NSAVC integer] [NSAVV integer] [NTRFrq integer]

[ILBFrq integer] [ISVFRQ integer] [NSAVL integer]

[IMGFrq integer] [IXTFrq integer]

[NLAT integer] [NSAVQ]

[NBLCkfep integer] [NSAVXyz integer] [MXYZ integer]

unit-spec::= [IUNCrd integer] [IUNRea integer] [IUNVel integer]

[IUNWri integer] [KUNIt integer] [CRAShu integer]

[BACKup integer] [IUNLdm integer] [IUNQ integer]

[ILAT integer] [IUNXyz integer]

[IBLCkfep integer]

[ILAP integer] [ILAF integer]

temperature-spec::= [FINAlt real] [FIRStt real] [TEMInc real]

[TSTRuc real] [TWINDH real] [TWINDL real]

[TBATh real]

options-spec::= [IASOrs integer] [IASVel integer] [ICHEcw integer]

[ISCAle integer] [ISCVel integer] [ISEEd repeat(integer)]

[SCALe real] [NDEGg integer] [RBUFfer real]

[AVERage] [ECHEck real] [TOL real]

cpt-spec::=

**»**pressurefour-dim-spec::= [FIL4dimension] [SKBOnd] [SKANgle]

[SKDIhedral] [SKVDerWaals] [SKELectrostatics]

[K4DInitial real] [INC4Dforce integer]

[DEC4Dforce integer] [MULTK4di real]

[E4FILLcoordinates real]

[FNLT4 real] [FSTT4 real] [TIN4 real]

[IHT4 integer] [IEQ4 integer] [ICH4 integer]

[TWH4 real] [TWL4 real]

Top

Options common to minimization and dynamics

The following table describes the keywords which apply to both

minimization and dynamics.

Keyword Default Purpose

NSTEP 100 The number of steps to be taken. This is the number of

dynamics steps which is also equal to the number of

energy evaluations.

INBFRQ 50 The frequency of regenerating the non-bonded list.

The list is regenerated if the current step number

modulo INBFRQ is zero and if INBFRQ is non-zero.

Specifying zero prevents the non-bonded list from being

regenerated at all.

INBFRQ = -1 --> all lists are updated when necessary

(heuristic test).

IHBFRQ 50 The frequency of regenerating the hydrogen bond list.

Analogous to INBFRQ

ILBFRQ 50 The frequency for checking whether an atom is in the

Langevin region, defined by RBUF, or not.

IMGFrq 0 The frequency for the image update (only used if IMAGES

or CRYSTAL is in use). The image update creates image atoms

needed for the energy computation from the list of allowed

symmetry transformations. Recommended value: 50, if a 2A

buffer is used between CUTIM and CUTNB.

IXTFrq 0 The frequency for the crystal update (only used of CRYSTAL

is in use). The crystal update generates a new list of

allowed symmetry transformations. This option is only

required if the size or shape of the periodic box (i.e. CPT)

can change during a simulation (or minimization).

Recommended value: 1000 (if running CPT dynamics).

non-bond- The specifications for generating the non-bonded list.

-spec

hbond- The specifications for generating the hydrogen bond list.

-spec

[ STRT ] STRT The dynamics is assumed to start from the input

[ ] coordinates using an assignment of velocities given by

[ ] IASVEL. No restart file is read.

[ REST ] The dynamics is restarted by reading the restart file

from unit IUNREA.

TIMESTP 0.001 Time step for dynamics in picoseconds. The default value

is 0.001 picoseconds.

VSENd false Flag to control brodcast of initial velocities from

zeroth process (mainly to compare parallel results

during development of the code)

IUNREA -1 Fortran unit from which the dynamics restart file should

be read. A value of -1 means don't read any file

IUNWRI -1 Fortran unit on which the dynamics restart file for

the present run is to be written. A value of -1 means

don't write any file. Formatted output.

IUNCRD -1 Fortran unit on which the coordinates of the dynamics run

are to be saved. A value of -1 means no coordinates should

be written. Unformatted output.

IUNXYZ -1 Fortran unit on which the coordinates,velocities,

and forces of the dynamics run are to be saved.

A value of -1 means no coordinates should

be written. Formatted output suitable for movies

with MOLDEN. Also for other high precision

debugging. Everything written to this unit is REAL*8

IUNLDM -1 Fortran unit on which the biasing potentials, the

histograms of the lambda variables of the dynamics

run are to be saved. A value of -1 means no histograms

should be written. Unformatted output (for details

see node: output).

IUNVEL -1 Fortran unit on which the velocities of the dynamics run

are to be saved. -1 means don't write. Unformatted output.

KUNIT -1 Fortran unit on which the total energy and some of its

components along with the temperature during the run are

written using formatted output.

CRASHU -1 Fortran unit where a single DCL command file will be

written. If the machine crashes before a restart file

is written, this file won't be touched. If the crash

occurs after a restart is written but before the run

completes, this file will contain the line, "$

@CRASH". If the run completes, the file will contain

the line, "$ @COMPLET". This allows for an automatic

recovery system after crashes.

IUNQ -1 Fortran unit on which values for charges (mostly QM/MM)

are to be saved. Mulliken charges are stored on as

X, Lowding charges as Y, and Merz-Kolman charges on Z

NSAVC 10 The step frequency for writing coordinates.

NSAVL 0 The step frequency for writing lambda histograms.

NSAVV 10 The step frequency for writing velocities.

NSAVQ 10 The step frequency for writing charges.

NSAVX 10 The step frequency for writing XYZ format file.

MXYZ -1 What is in the XYZ file. -1=nothing,0=energy only,1=coor,

2=coor+vel, 3=coor+vel+force,4=coor+force,5=coor,lambda,force.

All data are formatted with xE25.15 (except step # w/ -1).

NPRINT 10 The step frequency for storing on KUNIT as well as printing

on unit 6, the energy data of the dynamics run.

IPRFRQ 100 The step frequency for calculating averages and rms

fluctuations of the major energy values. If this

number is less than NTRFRQ and NTRFRQ is not equal to

0, square root of negative number errors will occur.

ISVFRQ NSTEP The step frequency for writing a restart file.

IHTFRQ 0 The step frequency for heating the molecule in increments

of TEMINC degrees in the heating portion of a dynamics

run. Zero means do no heating.

IEQFRQ 0 The step frequency for assigning or scaling velocities to

FINALT temperature during the equilibration stage of the

dynamics run.

NTRFRQ 0 The step frequency for stopping the rotation and translation

of the molecule during dynamics. This operation is done

automatically after any heating.

SEGSTR Flag (if present) that rotation and translation is stopped

based on segments. This is sometimes usefull for

replica when the whole system is replicated. Check

is provided for this.

FIRSTT 0.0 The initial temperature at which the velocities have to be

assigned at to begin the dynamics run. Important only

for the initial stage of a dynamics run.

FINALT 298.0 The desired final (equilibrium) temperature

for the system. Important for all stages except initiation.

TEMINC 5.0 The temperature increment to be given to the system every

IHTFRQ steps. Important in the heating stage.

TSTRUC -999. The temperature at which the starting structure has been

equilibrated. Used to assign velocities so that equal

partition of energy will yield the correct equilibrated

temperature. -999. is a default which causes the

program to assign velocities at T=1.25*FIRSTT.

TWINDH 10.0 The temperature deviation from FINALT to be allowed on the

high temperature side.(+ve). i.e. high side of the

temperature window. Useful during equilibration.

TWINDL -10.0 The temperature deviation from FINALT to be allowed on the

low temperature side.(-ve). i.e. low side of the

temperature window. Useful during equilibration.

TBATH FINALT The temperature of the heatbath in Langevin dynamics. When

set to zero it allows one to do purely dissipative

(quenched) dynamics.

RBUF 0.0 Inner radius of the buffer, or Langevin, region sphere. All

atoms with radial positions greater than RBUF angstroms are

propagated by Langevin dynamics, if the dynamics keyword

LANGevin has been specified.

IASORS 0 The option for scaling or assigning of velocities during

heating (every IHTFRQ steps) or equilibration

(every IEQFRQ steps). This keyword does not control

the initial assignment of velocities.

.eq. 0 - scale velocities. (use ISCVEL option)

.ne. 0 - assign velocities. (use IASVEL option)

IASVEL 1 The option for the choice of method for the assignment of

velocities during heating and equilibration when IASORS

is nonzero. This option also controls the initial

assignment of velocities (when not RESTart)

regardless of the IASORS value.

.eq. 0 - Use the comparison coordinate values

in AKMA units (sorry) with the STRT option.

If NTRFRQ is positive,

then net trans/rot will be removed first.

This option supresses other assignments of velocity.

.gt. 0 - gaussian distribution of velocity. (+ve)

.lt. 0 - uniform distribution of velocity. (-ve)

kinetic energy of 3N velocity components are same.

ISEED random The seed for the random number generator used for

assigning velocities. If not specified a value based on

the system clock is used; this is the recommended mode, since

it makes each run unique.

One integer, or as many as required by the random number

generator, may be specified.

ISCVEL 0 The option for two ways of scaling velocities.

.eq. 0 - single scale factor for all atoms

.ne. 0 - a scale factor for each atom proportional to the

kinetic energy average ratio between the system

and along every degree of freedom for that atom.

ICHECW 1 The option for checking to see if the average temperature

of the system lies within the allotted temperature window

(between FINALT+TWINDH and FINALT+TWINDL) every

IEQFRQ steps.

.eq. 0 - do not check

i.e. assign or scale velocities.

.ne. 0 - check window

i.e. assign or scale velocities only if average

temperature lies outside the window.

ISCALE 0 This option is to allow the user to scale the velocities

by a factor SCALE at the beginning of a restart run.

This may be useful in changing the desired temperature.

.eq. 0 no scaling done (usual input value)

.ne. 0 scale velocities by SCALE.

WARNING:

Please use this option only when you are changing the

temperature of the run.

SCALE 1. Scale factor for the previous option.

NDEGF computed Number of degrees of freedom to use in computing the

temperature. If not specified on any call, the value is

computed. This specification is not remembered between

successive calls to dynamics.

AVERAGE no When saving coordinates every NSAVC steps, this option will

cause the average structure of the last NSAVC dynamics steps

to be written instead of the final snapshot coordinate set.

This option is primarily used for making smooth movies.

ECHECK 20.0 The maximum amount the total energy may change on any step.

TOL 1.0E-10 The shake tolerance (if SHAKE is in use).

PCONst false Flag to indicate that constant pressure code will be used.

PINTernal true Flag to indicate that the internal pressure will be coupled

the reference pressure.

PEXTernal false Flag to indicate that the external pressure will be coupled

to the reference pressure.

PCOUpling 0.0 The coupling decay time in picoseconds for the pressure.

A good value for this is 5 ps.

COMPress 0.0 The compressibility in atm**-1. A good value for proteins

is 4.63e-5

PREFerence 1.0 The reference pressure in atmospheres.

VOLUme computed The volume in Angstroms**3 to use for the pressure

calculation denominator. This value is calculated if

the CRYStal feature is use.

TCONst false Flag to indicate that constant temperature code will be used.

TCOUpling 0.0 The coupling decay time in picoseconds for the temperature.

A good value for this is 5 ps.

TREFerence FINALT The reference temperature for constant temperature

simulations.

SGLD false Turn on SGMD/SGLD simulation.

Other SGLD parameters, such as TSGAVG, SGFT, TEMPSG, etc,

can be set to other than default values.

» sgld for more information.

SGBZ false Using SGMDfp/SGLDfp method for SGLD simulation to preserve

canonical ensemble.

MBOND Signifies that the dynamics run will be based on a

multi-body simulation. If no bodies have been

defined, this produces an error. Many of the

standard dynamics options retain their meaning, in

this case, but the following options are NOT

supported: SHAKE, CONSTANT PRESSURE, NOSE,

LEAPFROG, VER4, LANGEVIN.

description of the MBOND dynamics options.

NLAT 0 The step frequency for writing instantaneous lambda

temperature trajectories in lambda-dynamics.

NBLCkfep 0 The step frequency for writing the energy decompostion

trajectories in free energy calculation.

ILAT -1 Fortran unit on which the histograms of the lambda

temperature are to be saved. A value of -1 means no

histograms should be written.

IBLCkfep -1 Fortran unit on which the histograms of the energy

decomposition are to be saved. A value of -1 means no

histograms should be written. This file is used in post

processing in TSM module.

ILAP -1 Fortran unit on which the histograms of (Vi - Fi)

are to be saved. A value of -1 means no histograms

should be written. NSAVL is used for step frequency of

printing (Vi - Fi) information.

ILAF -1 Fortran unit on which the histograms of the restraining

potential are to be saved. A value of -1 means no histograms

should be written. NSAVL is used for step frequency of

printing the restraining potential.

Options common to minimization and dynamics

The following table describes the keywords which apply to both

minimization and dynamics.

Keyword Default Purpose

NSTEP 100 The number of steps to be taken. This is the number of

dynamics steps which is also equal to the number of

energy evaluations.

INBFRQ 50 The frequency of regenerating the non-bonded list.

The list is regenerated if the current step number

modulo INBFRQ is zero and if INBFRQ is non-zero.

Specifying zero prevents the non-bonded list from being

regenerated at all.

INBFRQ = -1 --> all lists are updated when necessary

(heuristic test).

IHBFRQ 50 The frequency of regenerating the hydrogen bond list.

Analogous to INBFRQ

ILBFRQ 50 The frequency for checking whether an atom is in the

Langevin region, defined by RBUF, or not.

IMGFrq 0 The frequency for the image update (only used if IMAGES

or CRYSTAL is in use). The image update creates image atoms

needed for the energy computation from the list of allowed

symmetry transformations. Recommended value: 50, if a 2A

buffer is used between CUTIM and CUTNB.

IXTFrq 0 The frequency for the crystal update (only used of CRYSTAL

is in use). The crystal update generates a new list of

allowed symmetry transformations. This option is only

required if the size or shape of the periodic box (i.e. CPT)

can change during a simulation (or minimization).

Recommended value: 1000 (if running CPT dynamics).

non-bond- The specifications for generating the non-bonded list.

-spec

**»**nbonds .hbond- The specifications for generating the hydrogen bond list.

-spec

**»**hbonds .[ STRT ] STRT The dynamics is assumed to start from the input

[ ] coordinates using an assignment of velocities given by

[ ] IASVEL. No restart file is read.

[ REST ] The dynamics is restarted by reading the restart file

from unit IUNREA.

TIMESTP 0.001 Time step for dynamics in picoseconds. The default value

is 0.001 picoseconds.

VSENd false Flag to control brodcast of initial velocities from

zeroth process (mainly to compare parallel results

during development of the code)

IUNREA -1 Fortran unit from which the dynamics restart file should

be read. A value of -1 means don't read any file

IUNWRI -1 Fortran unit on which the dynamics restart file for

the present run is to be written. A value of -1 means

don't write any file. Formatted output.

IUNCRD -1 Fortran unit on which the coordinates of the dynamics run

are to be saved. A value of -1 means no coordinates should

be written. Unformatted output.

IUNXYZ -1 Fortran unit on which the coordinates,velocities,

and forces of the dynamics run are to be saved.

A value of -1 means no coordinates should

be written. Formatted output suitable for movies

with MOLDEN. Also for other high precision

debugging. Everything written to this unit is REAL*8

IUNLDM -1 Fortran unit on which the biasing potentials, the

histograms of the lambda variables of the dynamics

run are to be saved. A value of -1 means no histograms

should be written. Unformatted output (for details

see node: output).

IUNVEL -1 Fortran unit on which the velocities of the dynamics run

are to be saved. -1 means don't write. Unformatted output.

KUNIT -1 Fortran unit on which the total energy and some of its

components along with the temperature during the run are

written using formatted output.

CRASHU -1 Fortran unit where a single DCL command file will be

written. If the machine crashes before a restart file

is written, this file won't be touched. If the crash

occurs after a restart is written but before the run

completes, this file will contain the line, "$

@CRASH". If the run completes, the file will contain

the line, "$ @COMPLET". This allows for an automatic

recovery system after crashes.

IUNQ -1 Fortran unit on which values for charges (mostly QM/MM)

are to be saved. Mulliken charges are stored on as

X, Lowding charges as Y, and Merz-Kolman charges on Z

NSAVC 10 The step frequency for writing coordinates.

NSAVL 0 The step frequency for writing lambda histograms.

NSAVV 10 The step frequency for writing velocities.

NSAVQ 10 The step frequency for writing charges.

NSAVX 10 The step frequency for writing XYZ format file.

MXYZ -1 What is in the XYZ file. -1=nothing,0=energy only,1=coor,

2=coor+vel, 3=coor+vel+force,4=coor+force,5=coor,lambda,force.

All data are formatted with xE25.15 (except step # w/ -1).

NPRINT 10 The step frequency for storing on KUNIT as well as printing

on unit 6, the energy data of the dynamics run.

IPRFRQ 100 The step frequency for calculating averages and rms

fluctuations of the major energy values. If this

number is less than NTRFRQ and NTRFRQ is not equal to

0, square root of negative number errors will occur.

ISVFRQ NSTEP The step frequency for writing a restart file.

IHTFRQ 0 The step frequency for heating the molecule in increments

of TEMINC degrees in the heating portion of a dynamics

run. Zero means do no heating.

IEQFRQ 0 The step frequency for assigning or scaling velocities to

FINALT temperature during the equilibration stage of the

dynamics run.

NTRFRQ 0 The step frequency for stopping the rotation and translation

of the molecule during dynamics. This operation is done

automatically after any heating.

SEGSTR Flag (if present) that rotation and translation is stopped

based on segments. This is sometimes usefull for

replica when the whole system is replicated. Check

is provided for this.

FIRSTT 0.0 The initial temperature at which the velocities have to be

assigned at to begin the dynamics run. Important only

for the initial stage of a dynamics run.

FINALT 298.0 The desired final (equilibrium) temperature

for the system. Important for all stages except initiation.

TEMINC 5.0 The temperature increment to be given to the system every

IHTFRQ steps. Important in the heating stage.

TSTRUC -999. The temperature at which the starting structure has been

equilibrated. Used to assign velocities so that equal

partition of energy will yield the correct equilibrated

temperature. -999. is a default which causes the

program to assign velocities at T=1.25*FIRSTT.

TWINDH 10.0 The temperature deviation from FINALT to be allowed on the

high temperature side.(+ve). i.e. high side of the

temperature window. Useful during equilibration.

TWINDL -10.0 The temperature deviation from FINALT to be allowed on the

low temperature side.(-ve). i.e. low side of the

temperature window. Useful during equilibration.

TBATH FINALT The temperature of the heatbath in Langevin dynamics. When

set to zero it allows one to do purely dissipative

(quenched) dynamics.

RBUF 0.0 Inner radius of the buffer, or Langevin, region sphere. All

atoms with radial positions greater than RBUF angstroms are

propagated by Langevin dynamics, if the dynamics keyword

LANGevin has been specified.

IASORS 0 The option for scaling or assigning of velocities during

heating (every IHTFRQ steps) or equilibration

(every IEQFRQ steps). This keyword does not control

the initial assignment of velocities.

.eq. 0 - scale velocities. (use ISCVEL option)

.ne. 0 - assign velocities. (use IASVEL option)

IASVEL 1 The option for the choice of method for the assignment of

velocities during heating and equilibration when IASORS

is nonzero. This option also controls the initial

assignment of velocities (when not RESTart)

regardless of the IASORS value.

.eq. 0 - Use the comparison coordinate values

in AKMA units (sorry) with the STRT option.

If NTRFRQ is positive,

then net trans/rot will be removed first.

This option supresses other assignments of velocity.

.gt. 0 - gaussian distribution of velocity. (+ve)

.lt. 0 - uniform distribution of velocity. (-ve)

kinetic energy of 3N velocity components are same.

ISEED random The seed for the random number generator used for

assigning velocities. If not specified a value based on

the system clock is used; this is the recommended mode, since

it makes each run unique.

One integer, or as many as required by the random number

generator, may be specified.

**»**randomISCVEL 0 The option for two ways of scaling velocities.

.eq. 0 - single scale factor for all atoms

.ne. 0 - a scale factor for each atom proportional to the

kinetic energy average ratio between the system

and along every degree of freedom for that atom.

ICHECW 1 The option for checking to see if the average temperature

of the system lies within the allotted temperature window

(between FINALT+TWINDH and FINALT+TWINDL) every

IEQFRQ steps.

.eq. 0 - do not check

i.e. assign or scale velocities.

.ne. 0 - check window

i.e. assign or scale velocities only if average

temperature lies outside the window.

ISCALE 0 This option is to allow the user to scale the velocities

by a factor SCALE at the beginning of a restart run.

This may be useful in changing the desired temperature.

.eq. 0 no scaling done (usual input value)

.ne. 0 scale velocities by SCALE.

WARNING:

Please use this option only when you are changing the

temperature of the run.

SCALE 1. Scale factor for the previous option.

NDEGF computed Number of degrees of freedom to use in computing the

temperature. If not specified on any call, the value is

computed. This specification is not remembered between

successive calls to dynamics.

AVERAGE no When saving coordinates every NSAVC steps, this option will

cause the average structure of the last NSAVC dynamics steps

to be written instead of the final snapshot coordinate set.

This option is primarily used for making smooth movies.

ECHECK 20.0 The maximum amount the total energy may change on any step.

TOL 1.0E-10 The shake tolerance (if SHAKE is in use).

PCONst false Flag to indicate that constant pressure code will be used.

PINTernal true Flag to indicate that the internal pressure will be coupled

the reference pressure.

PEXTernal false Flag to indicate that the external pressure will be coupled

to the reference pressure.

PCOUpling 0.0 The coupling decay time in picoseconds for the pressure.

A good value for this is 5 ps.

COMPress 0.0 The compressibility in atm**-1. A good value for proteins

is 4.63e-5

PREFerence 1.0 The reference pressure in atmospheres.

VOLUme computed The volume in Angstroms**3 to use for the pressure

calculation denominator. This value is calculated if

the CRYStal feature is use.

TCONst false Flag to indicate that constant temperature code will be used.

TCOUpling 0.0 The coupling decay time in picoseconds for the temperature.

A good value for this is 5 ps.

TREFerence FINALT The reference temperature for constant temperature

simulations.

SGLD false Turn on SGMD/SGLD simulation.

Other SGLD parameters, such as TSGAVG, SGFT, TEMPSG, etc,

can be set to other than default values.

» sgld for more information.

SGBZ false Using SGMDfp/SGLDfp method for SGLD simulation to preserve

canonical ensemble.

MBOND Signifies that the dynamics run will be based on a

multi-body simulation. If no bodies have been

defined, this produces an error. Many of the

standard dynamics options retain their meaning, in

this case, but the following options are NOT

supported: SHAKE, CONSTANT PRESSURE, NOSE,

LEAPFROG, VER4, LANGEVIN.

**»**mbond DynDesc for adescription of the MBOND dynamics options.

NLAT 0 The step frequency for writing instantaneous lambda

temperature trajectories in lambda-dynamics.

NBLCkfep 0 The step frequency for writing the energy decompostion

trajectories in free energy calculation.

ILAT -1 Fortran unit on which the histograms of the lambda

temperature are to be saved. A value of -1 means no

histograms should be written.

IBLCkfep -1 Fortran unit on which the histograms of the energy

decomposition are to be saved. A value of -1 means no

histograms should be written. This file is used in post

processing in TSM module.

ILAP -1 Fortran unit on which the histograms of (Vi - Fi)

are to be saved. A value of -1 means no histograms

should be written. NSAVL is used for step frequency of

printing (Vi - Fi) information.

ILAF -1 Fortran unit on which the histograms of the restraining

potential are to be saved. A value of -1 means no histograms

should be written. NSAVL is used for step frequency of

printing the restraining potential.

Top

Recommended CHARMM input for dynamics.

This section is intended only as a guide in setting up

a dynamics simulation input file. Changes should be made as necessary

according to personal tastes and project requirements.

1) For heating and early equilibration:

DYNAMICS LEAP VERLET RESTART(*) NSTEP 20000 TIMESTEP 0.001(+) -

IPRFRQ 1000 IHTFRQ 1000 IEQFRQ 5000 NTRFRQ 5000 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 100 NSAVC 100 NSAVV 0 INBFRQ 25 -

hbond-spec nonbond-spec -

FIRSTT 100.0 FINALT 300.0 TEMINC 100.0 -

IASORS 1 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 10.0 TWINDL -10.0

(*) Except for first run, the use STRT in place of RESTART

(+) If bonds to hydrogen atoms are SHAKEd

2) For late equilibration and analysis runs:

DYNAMICS LEAP VERLET RESTART NSTEP 20000 TIMESTEP 0.001 -

IPRFRQ 1000 IHTFRQ 2000 IEQFRQ 5000(*) NTRFRQ 5000 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 100 NSAVC 100 NSAVV 0 IHBFRQ 0 INBFRQ 25 -

hbond-spec nonbond-spec -

FIRSTT 100.0 FINALT 300.0 TEMINC 100.0 -

IASORS 0 IASVEL 1 ISCVEL 0 ICHECW 1 TWINDH 10.0 TWINDL -10.0

(*) Window checking should be disabled for the analysis run (i.e. IEQFRQ=0)

if you want a real microcanonical ensemble.

3) For heating, equilibration and analysis runs using Langevin dynamics:(+)

DYNA LEAP LANGEVIN STRT(*) NSTEP 20000 TIMESTEP 0.001 -

IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 0 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 100 NSAVC 100 NSAVV 0 IHBFRQ 0 INBFRQ 25 -

ILBFRQ 1000 RBUFFER 0.0 TBATH 300.0 -

hbond-spec nonbond-spec -

FIRSTT 300.0 FINALT 300.0 -

IASORS 0 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 0.0 TWINDL 0.0

(+) Note that the friction coefficients, in units of 1/ps, must first

be initialized by filling the array FBETA with the SCALAR command

SCALAR FBETA SET <real> <optional atom selection>

(*) Except for first run, the use STRT in place of RESTART

4) For quenched molecular dynamics:

For the first run (STRT), read velocities into the comparison

coordinate set, or this should directly follow a former dynamics command.

DYNA VERLET STRT(*) NSTEP 10000 TIMESTEP 0.001 -

IPRFRQ 1000 IHTFRQ 200 IEQFRQ 200 NTRFRQ 400 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 50 NSAVC 50 NSAVV 0 IHBFRQ 0 INBFRQ 25 -

hbond-spec nonbond-spec -

TSTRUC 300.0 FIRSTT 300.0 FINALT 0.0 TEMINC -30.0 -

IASORS 0 IASVEL 0 ISCVEL 0 ICHECW 1 TWINDH 0.0

or equivalently with Langevin (dissipative) dynamics

DYNA LANGEVIN STRT(*) NSTEP 10000 TIMESTEP 0.001 -

IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 4000 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 50 NSAVC 50 NSAVV 0 IHBFRQ 0 INBFRQ 25 -

hbond-spec nonbond-spec -

TSTRUC 300.0 FIRSTT 300.0 FINALT 300.0 -

ILBFRQ 1000 RBUFFER 0.0 TBATH 0.0 -

IASORS 1 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 0.0

(*) For first run, use RESTART otherwise

The IASVEL 0 option causes the comparison coordinates to be used

for the initial velocities (AKMA units).

For subsequent runs the options IASORS 1 and IASVEL 1 may be used

if random velocities are to be periodically assigned.

5) For constant temperature and/or pressure dynamics

DYNA LEAP VERLET STRT(*) NSTEP 20000 TIMESTEP 0.001 -

IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 0 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 100 NSAVC 100 NSAVV 0 IHBFRQ 0 INBFRQ 25 -

PCONst PINTernal COMPress 4.63e-5 PCOUpling 5.0 PREFerence 1.0 -

TCONst TCOUpling 5.0 TREFerence 300.0 -

hbond-spec nonbond-spec -

FIRSTT 300.0 FINALT 300.0 -

IASORS 0 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 0.0 TWINDL 0.0

6) For multi-body dynamics (assumes an atomistic equilibration has

already been performed, substructures defined and modes generated):

DYNA MBOND LOBA RESTART NSTEP 20000 TIMESTEP 0.001 -

IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 0 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 100 NSAVC 100 NSAVV 0 IHBFRQ 0 INBFRQ 25 -

TCONst TCOUpling 5.0 TREFerence 300.0 -

hbond-spec nonbond-spec -

FIRSTT 300.0 FINALT 300.0 -

MBPRlev -1

Recommended CHARMM input for dynamics.

This section is intended only as a guide in setting up

a dynamics simulation input file. Changes should be made as necessary

according to personal tastes and project requirements.

1) For heating and early equilibration:

DYNAMICS LEAP VERLET RESTART(*) NSTEP 20000 TIMESTEP 0.001(+) -

IPRFRQ 1000 IHTFRQ 1000 IEQFRQ 5000 NTRFRQ 5000 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 100 NSAVC 100 NSAVV 0 INBFRQ 25 -

hbond-spec nonbond-spec -

FIRSTT 100.0 FINALT 300.0 TEMINC 100.0 -

IASORS 1 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 10.0 TWINDL -10.0

(*) Except for first run, the use STRT in place of RESTART

(+) If bonds to hydrogen atoms are SHAKEd

2) For late equilibration and analysis runs:

DYNAMICS LEAP VERLET RESTART NSTEP 20000 TIMESTEP 0.001 -

IPRFRQ 1000 IHTFRQ 2000 IEQFRQ 5000(*) NTRFRQ 5000 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 100 NSAVC 100 NSAVV 0 IHBFRQ 0 INBFRQ 25 -

hbond-spec nonbond-spec -

FIRSTT 100.0 FINALT 300.0 TEMINC 100.0 -

IASORS 0 IASVEL 1 ISCVEL 0 ICHECW 1 TWINDH 10.0 TWINDL -10.0

(*) Window checking should be disabled for the analysis run (i.e. IEQFRQ=0)

if you want a real microcanonical ensemble.

3) For heating, equilibration and analysis runs using Langevin dynamics:(+)

DYNA LEAP LANGEVIN STRT(*) NSTEP 20000 TIMESTEP 0.001 -

IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 0 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 100 NSAVC 100 NSAVV 0 IHBFRQ 0 INBFRQ 25 -

ILBFRQ 1000 RBUFFER 0.0 TBATH 300.0 -

hbond-spec nonbond-spec -

FIRSTT 300.0 FINALT 300.0 -

IASORS 0 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 0.0 TWINDL 0.0

(+) Note that the friction coefficients, in units of 1/ps, must first

be initialized by filling the array FBETA with the SCALAR command

SCALAR FBETA SET <real> <optional atom selection>

(*) Except for first run, the use STRT in place of RESTART

4) For quenched molecular dynamics:

For the first run (STRT), read velocities into the comparison

coordinate set, or this should directly follow a former dynamics command.

DYNA VERLET STRT(*) NSTEP 10000 TIMESTEP 0.001 -

IPRFRQ 1000 IHTFRQ 200 IEQFRQ 200 NTRFRQ 400 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 50 NSAVC 50 NSAVV 0 IHBFRQ 0 INBFRQ 25 -

hbond-spec nonbond-spec -

TSTRUC 300.0 FIRSTT 300.0 FINALT 0.0 TEMINC -30.0 -

IASORS 0 IASVEL 0 ISCVEL 0 ICHECW 1 TWINDH 0.0

or equivalently with Langevin (dissipative) dynamics

DYNA LANGEVIN STRT(*) NSTEP 10000 TIMESTEP 0.001 -

IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 4000 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 50 NSAVC 50 NSAVV 0 IHBFRQ 0 INBFRQ 25 -

hbond-spec nonbond-spec -

TSTRUC 300.0 FIRSTT 300.0 FINALT 300.0 -

ILBFRQ 1000 RBUFFER 0.0 TBATH 0.0 -

IASORS 1 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 0.0

(*) For first run, use RESTART otherwise

The IASVEL 0 option causes the comparison coordinates to be used

for the initial velocities (AKMA units).

For subsequent runs the options IASORS 1 and IASVEL 1 may be used

if random velocities are to be periodically assigned.

5) For constant temperature and/or pressure dynamics

DYNA LEAP VERLET STRT(*) NSTEP 20000 TIMESTEP 0.001 -

IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 0 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 100 NSAVC 100 NSAVV 0 IHBFRQ 0 INBFRQ 25 -

PCONst PINTernal COMPress 4.63e-5 PCOUpling 5.0 PREFerence 1.0 -

TCONst TCOUpling 5.0 TREFerence 300.0 -

hbond-spec nonbond-spec -

FIRSTT 300.0 FINALT 300.0 -

IASORS 0 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 0.0 TWINDL 0.0

6) For multi-body dynamics (assumes an atomistic equilibration has

already been performed, substructures defined and modes generated):

DYNA MBOND LOBA RESTART NSTEP 20000 TIMESTEP 0.001 -

IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 0 -

IUNREA 30 IUNWRI 31 IUNCRD 50 IUNVEL -1 KUNIT 70 -

NPRINT 100 NSAVC 100 NSAVV 0 IHBFRQ 0 INBFRQ 25 -

TCONst TCOUpling 5.0 TREFerence 300.0 -

hbond-spec nonbond-spec -

FIRSTT 300.0 FINALT 300.0 -

MBPRlev -1

Top

Running Molecular Dynamics

The theoretical basis for dynamical simulations is elementary

physics. The force on a particle is equal to the negative gradient of

the potential energy of the particle. CHARMM can solve this equation

numerically for all atoms in the molecule. A simple second order predictor

two step method due to Verlet is used for integration.

The choice of the integration step size is very important.

One must weigh the increased accuracy of using a small step size against

the longer real time that can be simulated with a given amount of

execution time when a larger step size is used. The time step may be

entered in picoseconds (using the TIMESTP keyword).

CHARMM provides information on the accuracy of the numerical

solution. Since the system has no external forces, the total energy

should be conserved. Numerical errors will result in some fluctuations

in the total energy so a good test is to compare the fluctuations in

total energy to the fluctuations in kinetic energy as these fluctuations

are proportional to the heat capacity of the system. See the next node

for a description of dynamics output.

Because the force constants for the bonds and bond angles are

fairly large, it is reasonable under certain circumstances to constrain

their values during dynamics. Such constraints are applicable if the

harmonic motions are weakly coupled to other motions. The advantage of

such constraints is that the step size of the numerical integration may

be increased without sacrificing accuracy as these terms have the

largest gradients in macromolecules simulated at physiological

temperatures. We use the SHAKE algorithm for applying the constraints,

the bonds involved with hydrogens, all bonds, all bonds and the angles

involving hydrogens, or all bonds and angles.

A dynamics run has basically four parts; initialization,

heating, equilibration, and the simulation itself. Initialization means

providing an initial position and velocity for all the atoms. Heating is

the process of increasing the kinetic energy of the system up to a final

temperature at which the simulation will be conducted. Equilibration is

the process where the kinetic energy and the potential energy of the

system evenly distribute themselves throughout the system. Only when the

average temperature of the system stabilizes can one collect the

trajectory information for analysis.

The initial coordinates of a simulation are obtained after

applying the minimization algorithm to a complete coordinate set. One

cannot start with a system with a large potential energy as it will

quickly heat up to unreasonable temperatures. For initializing the

velocities, the user can specify velocities from the comparison coordinates

(IASVEL 0), a uniform distribution of kinetic energy along each coordinate

with random sign of the motion along each axis (IASVEL -1) or a

Gaussian distribution of velocities (IASVEL 1 the default). The temperature

at which velocities are assigned is determined by FIRSTT and TSTRUC

by the algorithm:

Tassign = 2*(FIRSTT-TSTRUC) + TSTRUC.

For a harmonic system equilibrated to TSTRUC equal partition of the

energy will result in an equilibrated temperature of roughly FIRSTT.

If TSTRUC is not specified 1.25*FIRSTT will be used for assignment.

Velocities may also be passed to dynamics in the comparison

coordinate set (as opposed to assignment). This allows the user

considerable flexibility in setting up the initial conditions.

The heating of system is performed gently by increasing the

kinetic energy by a small amount periodically. The number of integration

steps between heating applications, the final temperature, and the

kinetic energy increment are all user specified. In addition, there is a

choice in the method of increasing the kinetic energy of the system. One

may scale existing velocities or reassign them. The velocities can be

scaled by either one scale factor calculated for the kinetic energy of

the system averaged over many time steps or by scale factors established

for each atom base ed on the ratio of its time averaged kinetic energy

with that of the system. If reassignment is chosen, the velocities can

have either a uniform or Gaussian distribution.

To equilibrate the structure, one can specify a window around

the final temperature where velocity adjustments will be made. The

choice of velocity adjustments is the same as described above for

heating.

For the actual run, CHARMM will output the position and

velocities of all atoms at intervals specified by the user. The

temperature window can be set larger so that any gross conformational

changes which result in a different potential energy will cause the

temperature to be maintained.

At any time energy is added to the system, the angular momentum

of the system will be reduced to zero and translational motion will be

stopped. One can also request that these operations be performed at any

time during the dynamics run.

The use of a restart file is essential for running dynamics.

The restart file contains information about the most recent coordinate

sets necessary for the VERLET algorithm. In addition the values of

the energy accumulators are stored. All other information (such as

SHAKE, fixed atoms, harmonic constraints, friction coefficients) has

to be regenerated before invoking a dynamics restart.

When the run is initiated, a restart file must be written using

the IUNWRI keyword. As the dynamics routine complete NCYCLE,

Output::, steps of dynamics, the Fortran unit specified by IUNWRI will

be rewound and a restart file will be written. In case of crashes, one

has restart files corresponding to various points in the run. The CRASHU

variable may prove valuable. Successive runs of CHARMM to continue the

dynamics run must read the previous restart file using the IUNREA

keyword and write it out for the next part of the run.

Restarts may be done to reset various options, or to break up a long run

into several shorter runs. Restart files will only run with the version

of CHARMM they are created with.

There are many numbers giving the frequency of actions to be

taken during dynamics such as updating the non-bonded list, heating the

molecule etc. Some of these numbers are adjusted along with the number

of steps to run so that numbers all have a common divisor. At the

present time, there are combinations which result in errors. At some

point an attempt may be made to catalog all the actions, and check for

erroneous processing.

If one is interested in simulating the motion of part of the

system with the rest of the system remaining fixed, it is possible to

fix atoms in place,

is done, there are several effect on the dynamics. First, since the

system is now anchored in space, the center of mass motion and total

angular velocity is never stopped. Second, the number of degrees of

freedom used for calculating the temperature is set to the number of

free atoms times 3 minus 6. Third, the coordinate and velocity

trajectory files will contain the position of the fixed atoms only

once, and all other records will hold just the moving atoms. This

saves a great deal of disk space.

Trajectory files can be merged, broken in smaller pieces, and

sampled at different intervals. Likewise, said operations can be

performed on coordinate trajectories while rotating the coordinates to

match a given coordinate set.

When the DYNAmics command exits, the main coordinate set

contains the final coordinate positions from the last energy evaluation and

the comparison coordinates will contain the final velocities In AKMA units.

Finally, a brief discussion of the Langevin dynamics algorithm is

presented. The Langevin dynamics algorithm presently in CHARMM was intented

to be used primarily with the "Stochastic Boundary Molecular Dynamics" method

and consequently has been restricted to an algorithm which is valid only for

the case FBETA*TIMESTEP<<1.0. That is for cases where relatively small

friction coefficients are used. Typically values of FBETA*TIMESTEP up to

about 0.3 still produce a stable dynamics which also satisfy the

fluctuation-dissipation theorem.

The algorithm itself reduces to the Verlet algorithm when FBETA is

zero and consequently may be used to do regular dynamics, actually it is

the same routine which does both dynamics.

In using Langevin dynamics care must be taken to first initialize

the array FBETA by using the scalar commands e.g.,

CHARMM >SCALAR FBETA SET <real> <atom selection>

Failure to do this just means you are doing regular dynamics so no warning is

given by CHARMM.

Running Molecular Dynamics

The theoretical basis for dynamical simulations is elementary

physics. The force on a particle is equal to the negative gradient of

the potential energy of the particle. CHARMM can solve this equation

numerically for all atoms in the molecule. A simple second order predictor

two step method due to Verlet is used for integration.

The choice of the integration step size is very important.

One must weigh the increased accuracy of using a small step size against

the longer real time that can be simulated with a given amount of

execution time when a larger step size is used. The time step may be

entered in picoseconds (using the TIMESTP keyword).

CHARMM provides information on the accuracy of the numerical

solution. Since the system has no external forces, the total energy

should be conserved. Numerical errors will result in some fluctuations

in the total energy so a good test is to compare the fluctuations in

total energy to the fluctuations in kinetic energy as these fluctuations

are proportional to the heat capacity of the system. See the next node

for a description of dynamics output.

Because the force constants for the bonds and bond angles are

fairly large, it is reasonable under certain circumstances to constrain

their values during dynamics. Such constraints are applicable if the

harmonic motions are weakly coupled to other motions. The advantage of

such constraints is that the step size of the numerical integration may

be increased without sacrificing accuracy as these terms have the

largest gradients in macromolecules simulated at physiological

temperatures. We use the SHAKE algorithm for applying the constraints,

**»**cons SHAKE. SHAKE can be applied to justthe bonds involved with hydrogens, all bonds, all bonds and the angles

involving hydrogens, or all bonds and angles.

A dynamics run has basically four parts; initialization,

heating, equilibration, and the simulation itself. Initialization means

providing an initial position and velocity for all the atoms. Heating is

the process of increasing the kinetic energy of the system up to a final

temperature at which the simulation will be conducted. Equilibration is

the process where the kinetic energy and the potential energy of the

system evenly distribute themselves throughout the system. Only when the

average temperature of the system stabilizes can one collect the

trajectory information for analysis.

The initial coordinates of a simulation are obtained after

applying the minimization algorithm to a complete coordinate set. One

cannot start with a system with a large potential energy as it will

quickly heat up to unreasonable temperatures. For initializing the

velocities, the user can specify velocities from the comparison coordinates

(IASVEL 0), a uniform distribution of kinetic energy along each coordinate

with random sign of the motion along each axis (IASVEL -1) or a

Gaussian distribution of velocities (IASVEL 1 the default). The temperature

at which velocities are assigned is determined by FIRSTT and TSTRUC

by the algorithm:

Tassign = 2*(FIRSTT-TSTRUC) + TSTRUC.

For a harmonic system equilibrated to TSTRUC equal partition of the

energy will result in an equilibrated temperature of roughly FIRSTT.

If TSTRUC is not specified 1.25*FIRSTT will be used for assignment.

Velocities may also be passed to dynamics in the comparison

coordinate set (as opposed to assignment). This allows the user

considerable flexibility in setting up the initial conditions.

The heating of system is performed gently by increasing the

kinetic energy by a small amount periodically. The number of integration

steps between heating applications, the final temperature, and the

kinetic energy increment are all user specified. In addition, there is a

choice in the method of increasing the kinetic energy of the system. One

may scale existing velocities or reassign them. The velocities can be

scaled by either one scale factor calculated for the kinetic energy of

the system averaged over many time steps or by scale factors established

for each atom base ed on the ratio of its time averaged kinetic energy

with that of the system. If reassignment is chosen, the velocities can

have either a uniform or Gaussian distribution.

To equilibrate the structure, one can specify a window around

the final temperature where velocity adjustments will be made. The

choice of velocity adjustments is the same as described above for

heating.

For the actual run, CHARMM will output the position and

velocities of all atoms at intervals specified by the user. The

temperature window can be set larger so that any gross conformational

changes which result in a different potential energy will cause the

temperature to be maintained.

At any time energy is added to the system, the angular momentum

of the system will be reduced to zero and translational motion will be

stopped. One can also request that these operations be performed at any

time during the dynamics run.

The use of a restart file is essential for running dynamics.

The restart file contains information about the most recent coordinate

sets necessary for the VERLET algorithm. In addition the values of

the energy accumulators are stored. All other information (such as

SHAKE, fixed atoms, harmonic constraints, friction coefficients) has

to be regenerated before invoking a dynamics restart.

When the run is initiated, a restart file must be written using

the IUNWRI keyword. As the dynamics routine complete NCYCLE,

Output::, steps of dynamics, the Fortran unit specified by IUNWRI will

be rewound and a restart file will be written. In case of crashes, one

has restart files corresponding to various points in the run. The CRASHU

variable may prove valuable. Successive runs of CHARMM to continue the

dynamics run must read the previous restart file using the IUNREA

keyword and write it out for the next part of the run.

Restarts may be done to reset various options, or to break up a long run

into several shorter runs. Restart files will only run with the version

of CHARMM they are created with.

There are many numbers giving the frequency of actions to be

taken during dynamics such as updating the non-bonded list, heating the

molecule etc. Some of these numbers are adjusted along with the number

of steps to run so that numbers all have a common divisor. At the

present time, there are combinations which result in errors. At some

point an attempt may be made to catalog all the actions, and check for

erroneous processing.

If one is interested in simulating the motion of part of the

system with the rest of the system remaining fixed, it is possible to

fix atoms in place,

**»**cons fixed atom. If thisis done, there are several effect on the dynamics. First, since the

system is now anchored in space, the center of mass motion and total

angular velocity is never stopped. Second, the number of degrees of

freedom used for calculating the temperature is set to the number of

free atoms times 3 minus 6. Third, the coordinate and velocity

trajectory files will contain the position of the fixed atoms only

once, and all other records will hold just the moving atoms. This

saves a great deal of disk space.

Trajectory files can be merged, broken in smaller pieces, and

sampled at different intervals. Likewise, said operations can be

performed on coordinate trajectories while rotating the coordinates to

match a given coordinate set.

When the DYNAmics command exits, the main coordinate set

contains the final coordinate positions from the last energy evaluation and

the comparison coordinates will contain the final velocities In AKMA units.

Finally, a brief discussion of the Langevin dynamics algorithm is

presented. The Langevin dynamics algorithm presently in CHARMM was intented

to be used primarily with the "Stochastic Boundary Molecular Dynamics" method

and consequently has been restricted to an algorithm which is valid only for

the case FBETA*TIMESTEP<<1.0. That is for cases where relatively small

friction coefficients are used. Typically values of FBETA*TIMESTEP up to

about 0.3 still produce a stable dynamics which also satisfy the

fluctuation-dissipation theorem.

The algorithm itself reduces to the Verlet algorithm when FBETA is

zero and consequently may be used to do regular dynamics, actually it is

the same routine which does both dynamics.

In using Langevin dynamics care must be taken to first initialize

the array FBETA by using the scalar commands e.g.,

CHARMM >SCALAR FBETA SET <real> <atom selection>

Failure to do this just means you are doing regular dynamics so no warning is

given by CHARMM.

Top

Contents of a dynamics output

Note: This description of the output of a command is not

normally going to be part of the documentation of commands. The dynamics

output is sufficiently confusing that this description is necessary.

The first part of CHARMM's output after a dynamics command lists

all of the options that apply to that part of the run. Then, any

information about velocity assignments (temperature changes) follows.

Any time the velocities are changed in an anisotropic way, the motion of

and about the center of mass will be stopped. This results in a printout

both before and after this operation of the "DETAILS ABOUT CENTRE OF

MASS". Its position and velocity are output followed by the components

of the angular momentum. The last line gives the translation kinetic

energy of the system, and thus one should expect a drop in the total

energy and temperature of the system afterwards.

Non-bonded interaction and hydrogen bond updates will appear

intermittently and are cleared labeled.

Every NPRINT steps, the total energy and various contributions

will be printed. This output is preceded by a title which gives the

correspondence of numbers to energy names. After IPRFRQ steps will

appear the averages and RMS fluctuations. After the second such printout

of averages and RMS fluctuations, the averages and RMS fluctuations for

the run upto the last turning of the molecule will be given. This gives

you longer range statistics. Such a calculation will not be done if

IPRFRQ equals NTRFRQ. The ratio of total energy to kinetic energy

fluctuations is an excellent measure of the accuracy of the run.

After the averages are printed, a least squares fit of the total

energy against the step number will be made to look for drift in the

energy. Two such values are printed, one for the last IPRFRQ steps, and

one to the previous turn. Next, the initial energy for the statistics,

both short range and long, are printed. Finally, the correlation

coefficient of the energy versus step is given for both ranges. A value

close to zero indicates no systematic drift; a magnitude near 1 means

you have a real problem with the dynamics.

This process of printout continues until the end of the run is

reached. Just before the last energy is printed will appear a message

about the writing of coordinates and velocities to their respective

files.

Output of the lambda dynamics and post-processing

(a) Output

The output of the lambda dynamics, i.e. the histograms and

the biasing potentials on the lambda variables, is written in a

separate file from the coordinate file.

To specify the output fortran unit and the writing frequency,

keywords IUNLDM and NSAVL are used. They are treated in the same fashion

as IUNCRD and NSAVC.

There is no separate restart file for the lambda dynamics. The

information necessary for restarting a lambda dynamics is included

at the end of a regular dynamic restart file. Thus, to restart the

lambda dynamics is exactly same as restarting a regular dynamics run

except you have to specify IUNLDM and NSAVL. E.g

!input title for lambda i/o

LDTITLE

* This is a test

* output for lambdas

open unit 11 writ form name output_file

open unit 12 read form name input_file

open unit 15 writ file name histogram

dyna rest leap time 0.001 -

nstep 10 nprint 1 iprfrq 10 -

iunrea 12 iunwri 11 iuncrd -1 nsavc 1 IUNLdm 15 NSAVL 5 -

first 300. -

inbfrq 40 nbxmod 5 atom cdie shif vatom vdist vshif -

cutnb 8. ctofnb 7.5 ctonnb 6.5 eps 1. e14fac 0.4 wmin 1.5 -

cutim 8. imgfrq 40

The file is in binary output, but the order of the standard

lambda-dynamics output is very similar to a regular output file:

header information:

(1) header=LAMB, icntrl (automatically written)

(2) title

(3) total no. of biasing potentials

(4) form of each biasing potential (total = Nbias)

(5) total no. of blocks

at each NSAVL:

(6) lambda**2 (total = No. of blocks)

Multi-Site lambda-dynamics output is also quite similar:

header information:

(1) header=MSLD, icntrl (automatically written)

(2) title

(3) total no. of biasing potentials

(4) form of each biasing potential

(total = no. of biasing potentials)

(5) value of each fixed bias (total = total no. of blocks)

(6) site number for each block

(total = total no. of blocks; Site(1)=1)

(7) lambda temperature

(assigned from LANG TEMP lam_temp in BLOCK setup)

at each NSAVL:

(8) lambda(i) (total = total no. of blocks)

(9) theta(i,j)

(if functional form F2EXp or F2SIn, total = total no. of sites)

(if functional form FNExp or FNSIn, total = total no. of blocks)

Parallel to a regular coordinate file of the dynamic run, the

unformatted lambda dynamics output file will automatically include a

header and an integer array providing information on the values of NSTEP,

NSAVL, NPRIV etc. In Multi-Site lambda-dynamics (MSLD), this array also

includes: the total number of blocks, degrees of freedom with respect to

lambda, the total number of Sites and an identifier for the functional

form of lambda used to generate the trajectory.

Integer array values in lambda-dynamics and MSLD.

(** indicates use in MSLD only)

ICNTRL(1) = nfile, unit number for lambda file

ICNTRL(2) = npriv

ICNTRL(3) = nsavl, interval for saving lambda values

ICNTRL(4) = nstep, total no. of steps

ICNTRL(5) =

ICNTRL(6) =

ICNTRL(7) = total no. of blocks **

ICNTRL(8) = lambda degrees of freedom **

ICNTRL(9) =

ICNTRL(10) =

ICNTRL(11) = total no. of Sites **

ICNTRL(12) = 2 (if F2SIn or F2EXp), 0 (if FNSIn or FNEXp) **

ICNTRL(13)

...

ICNTRL(20)

To name a title for the output file (in complying with

the CHARMM file requirement), the command LDTItle (similar to TITLE

command) can be used. E.g.

LDTItle

* mte: Methanol to ethane

* output for lambda dynamics

will write out a title before any other output data.

The information on biasing potentials will also be written out.

It takes a similar form as they were read in (see BLOCK.DOC), i.e.

INTEGER : total No. of biasing potentials.

I J CLASS REF CFORCE NPOWER : the format for each biasing potential.

The number of blocks are included here in standard lambda-dynamics,

but was moved to ICNTRL(7) in Multi-Site lambda-dynamics:

INTEGER : the total no. of blocks.

If Multi-Site lambda-dynamics (MSLD) is used then the temperature

and the fixed biases on each block are also written:

INTEGER : Site(i)+1 (i=1, total no. of blocks; Site(1)=0)

REAL : temperature

The remaining output consists of the lambda values.

For standard lambda-dynamics and theta lambda-dynamics, the format is:

REAL : lambda(i)^2 (i=1, total no. of blocks)

For theta dynamics, theta values are included in the format:

REAL : theta

For Multi-Site lambda-dynamics, lambda and theta values are included:

REAL : lambda(i) (i=1, total no. of blocks)

REAL : theta(Site_a,Sub_j) (a=1, total no. of Sites;

j=1, total no. of Blocks on Site_a)

(b) Post-processing MSLD lambda trajectory files

The Multi-Site lambda-dynamics output files can be analyzed by the

TRAJectory LAMBda command once the lambda trajectory file is opened:

e.g.

open unit 14 read file name prod.lmd

traj lamb print ctlo 0.8 cthi 0.90 first 14 nunit 1

TRAJectory LAMB {read-spec}

read-spec := [FIRST unit] [NUNIt int] [SKIP int]

[BEGIN int] [STOP int]

FIRStunit (IREAd) - first unit from which to read

NUNIts (NREAd) - number of units from which to read (default: 1)

SKIP - skip value for both reading and writing (default: 1)

Other options are:

PRINt - print lambda and theta values to output file

CTLO - first threshold for approximating lambda = 1 (default: 0.8)

CTHI - second threshold for approximating lambda = 1 (default: 0.9)

TEMP - temperature for calculating relative free energies from

populations (default: read in from trajectory file)

QUERy - print header information only

NOSUb - suppress the storage of internal CHARMM variables

The output provides a summary of statistics from the lambda

populations for the two threshold values:

(1) Total Population Count for each Block (i.e. how often each

block i has lambda(i) > threshold)

(2) Total number of transitions between dominant blocks at each Site

as well as the overall transition rate (in units of 1/ps).

(3) Free energy differences between individual blocks at each Site

(with and without taking into account the fixed biases, lambdaF)

For systems with two sites (ie. with multiple blocks at two Sites)

(4) Total Population Count for each Ligand (unique combination of

dominant blocks)

(5) Free energy differences between individual Ligands

(with and without taking into account the fixed biases, lambdaF)

(6) Fraction Physical Ligand represents the fraction of the snapshots

that represent a "physical ligand", that is, where

lambda(i) > threshold for one block i at every Site.

See testcase in: test/c36test/msld_test1.inp for examples of

setting up and analyzing Multi-Site lambda-dynamics simulations and

trajectories.

END

Contents of a dynamics output

Note: This description of the output of a command is not

normally going to be part of the documentation of commands. The dynamics

output is sufficiently confusing that this description is necessary.

The first part of CHARMM's output after a dynamics command lists

all of the options that apply to that part of the run. Then, any

information about velocity assignments (temperature changes) follows.

Any time the velocities are changed in an anisotropic way, the motion of

and about the center of mass will be stopped. This results in a printout

both before and after this operation of the "DETAILS ABOUT CENTRE OF

MASS". Its position and velocity are output followed by the components

of the angular momentum. The last line gives the translation kinetic

energy of the system, and thus one should expect a drop in the total

energy and temperature of the system afterwards.

Non-bonded interaction and hydrogen bond updates will appear

intermittently and are cleared labeled.

Every NPRINT steps, the total energy and various contributions

will be printed. This output is preceded by a title which gives the

correspondence of numbers to energy names. After IPRFRQ steps will

appear the averages and RMS fluctuations. After the second such printout

of averages and RMS fluctuations, the averages and RMS fluctuations for

the run upto the last turning of the molecule will be given. This gives

you longer range statistics. Such a calculation will not be done if

IPRFRQ equals NTRFRQ. The ratio of total energy to kinetic energy

fluctuations is an excellent measure of the accuracy of the run.

After the averages are printed, a least squares fit of the total

energy against the step number will be made to look for drift in the

energy. Two such values are printed, one for the last IPRFRQ steps, and

one to the previous turn. Next, the initial energy for the statistics,

both short range and long, are printed. Finally, the correlation

coefficient of the energy versus step is given for both ranges. A value

close to zero indicates no systematic drift; a magnitude near 1 means

you have a real problem with the dynamics.

This process of printout continues until the end of the run is

reached. Just before the last energy is printed will appear a message

about the writing of coordinates and velocities to their respective

files.

Output of the lambda dynamics and post-processing

(a) Output

The output of the lambda dynamics, i.e. the histograms and

the biasing potentials on the lambda variables, is written in a

separate file from the coordinate file.

To specify the output fortran unit and the writing frequency,

keywords IUNLDM and NSAVL are used. They are treated in the same fashion

as IUNCRD and NSAVC.

There is no separate restart file for the lambda dynamics. The

information necessary for restarting a lambda dynamics is included

at the end of a regular dynamic restart file. Thus, to restart the

lambda dynamics is exactly same as restarting a regular dynamics run

except you have to specify IUNLDM and NSAVL. E.g

!input title for lambda i/o

LDTITLE

* This is a test

* output for lambdas

open unit 11 writ form name output_file

open unit 12 read form name input_file

open unit 15 writ file name histogram

dyna rest leap time 0.001 -

nstep 10 nprint 1 iprfrq 10 -

iunrea 12 iunwri 11 iuncrd -1 nsavc 1 IUNLdm 15 NSAVL 5 -

first 300. -

inbfrq 40 nbxmod 5 atom cdie shif vatom vdist vshif -

cutnb 8. ctofnb 7.5 ctonnb 6.5 eps 1. e14fac 0.4 wmin 1.5 -

cutim 8. imgfrq 40

The file is in binary output, but the order of the standard

lambda-dynamics output is very similar to a regular output file:

header information:

(1) header=LAMB, icntrl (automatically written)

(2) title

(3) total no. of biasing potentials

(4) form of each biasing potential (total = Nbias)

(5) total no. of blocks

at each NSAVL:

(6) lambda**2 (total = No. of blocks)

Multi-Site lambda-dynamics output is also quite similar:

header information:

(1) header=MSLD, icntrl (automatically written)

(2) title

(3) total no. of biasing potentials

(4) form of each biasing potential

(total = no. of biasing potentials)

(5) value of each fixed bias (total = total no. of blocks)

(6) site number for each block

(total = total no. of blocks; Site(1)=1)

(7) lambda temperature

(assigned from LANG TEMP lam_temp in BLOCK setup)

at each NSAVL:

(8) lambda(i) (total = total no. of blocks)

(9) theta(i,j)

(if functional form F2EXp or F2SIn, total = total no. of sites)

(if functional form FNExp or FNSIn, total = total no. of blocks)

Parallel to a regular coordinate file of the dynamic run, the

unformatted lambda dynamics output file will automatically include a

header and an integer array providing information on the values of NSTEP,

NSAVL, NPRIV etc. In Multi-Site lambda-dynamics (MSLD), this array also

includes: the total number of blocks, degrees of freedom with respect to

lambda, the total number of Sites and an identifier for the functional

form of lambda used to generate the trajectory.

Integer array values in lambda-dynamics and MSLD.

(** indicates use in MSLD only)

ICNTRL(1) = nfile, unit number for lambda file

ICNTRL(2) = npriv

ICNTRL(3) = nsavl, interval for saving lambda values

ICNTRL(4) = nstep, total no. of steps

ICNTRL(5) =

ICNTRL(6) =

ICNTRL(7) = total no. of blocks **

ICNTRL(8) = lambda degrees of freedom **

ICNTRL(9) =

ICNTRL(10) =

ICNTRL(11) = total no. of Sites **

ICNTRL(12) = 2 (if F2SIn or F2EXp), 0 (if FNSIn or FNEXp) **

ICNTRL(13)

...

ICNTRL(20)

To name a title for the output file (in complying with

the CHARMM file requirement), the command LDTItle (similar to TITLE

command) can be used. E.g.

LDTItle

* mte: Methanol to ethane

* output for lambda dynamics

will write out a title before any other output data.

The information on biasing potentials will also be written out.

It takes a similar form as they were read in (see BLOCK.DOC), i.e.

INTEGER : total No. of biasing potentials.

I J CLASS REF CFORCE NPOWER : the format for each biasing potential.

The number of blocks are included here in standard lambda-dynamics,

but was moved to ICNTRL(7) in Multi-Site lambda-dynamics:

INTEGER : the total no. of blocks.

If Multi-Site lambda-dynamics (MSLD) is used then the temperature

and the fixed biases on each block are also written:

INTEGER : Site(i)+1 (i=1, total no. of blocks; Site(1)=0)

REAL : temperature

The remaining output consists of the lambda values.

For standard lambda-dynamics and theta lambda-dynamics, the format is:

REAL : lambda(i)^2 (i=1, total no. of blocks)

For theta dynamics, theta values are included in the format:

REAL : theta

For Multi-Site lambda-dynamics, lambda and theta values are included:

REAL : lambda(i) (i=1, total no. of blocks)

REAL : theta(Site_a,Sub_j) (a=1, total no. of Sites;

j=1, total no. of Blocks on Site_a)

(b) Post-processing MSLD lambda trajectory files

The Multi-Site lambda-dynamics output files can be analyzed by the

TRAJectory LAMBda command once the lambda trajectory file is opened:

e.g.

open unit 14 read file name prod.lmd

traj lamb print ctlo 0.8 cthi 0.90 first 14 nunit 1

TRAJectory LAMB {read-spec}

read-spec := [FIRST unit] [NUNIt int] [SKIP int]

[BEGIN int] [STOP int]

FIRStunit (IREAd) - first unit from which to read

NUNIts (NREAd) - number of units from which to read (default: 1)

SKIP - skip value for both reading and writing (default: 1)

Other options are:

PRINt - print lambda and theta values to output file

CTLO - first threshold for approximating lambda = 1 (default: 0.8)

CTHI - second threshold for approximating lambda = 1 (default: 0.9)

TEMP - temperature for calculating relative free energies from

populations (default: read in from trajectory file)

QUERy - print header information only

NOSUb - suppress the storage of internal CHARMM variables

The output provides a summary of statistics from the lambda

populations for the two threshold values:

(1) Total Population Count for each Block (i.e. how often each

block i has lambda(i) > threshold)

(2) Total number of transitions between dominant blocks at each Site

as well as the overall transition rate (in units of 1/ps).

(3) Free energy differences between individual blocks at each Site

(with and without taking into account the fixed biases, lambdaF)

For systems with two sites (ie. with multiple blocks at two Sites)

(4) Total Population Count for each Ligand (unique combination of

dominant blocks)

(5) Free energy differences between individual Ligands

(with and without taking into account the fixed biases, lambdaF)

(6) Fraction Physical Ligand represents the fraction of the snapshots

that represent a "physical ligand", that is, where

lambda(i) > threshold for one block i at every Site.

See testcase in: test/c36test/msld_test1.inp for examples of

setting up and analyzing Multi-Site lambda-dynamics simulations and

trajectories.

END

Top

Reading and writing trajectory frames with direct commands

This facility allows the creation or manipulation of trajectory files

The main uses of this facility are;

1) creating artificial trajectory files from coordinate frames

2) reading an existing trajectory frame by frame for analysis that

requires access to a variety of CHARMM commands

3) modifying an existing trajectory (copy with changes) such as

minimizing each frame or other operations.

Handling trajectories stored in multiple files

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

All CHARMM commands and routines that can read trajectories use the same

syntax to specify how the trajectory should be read. For trajectories stored

in multiple files CHARMM checks that the files form a contiguous trajectory

(no overlaps or missing pieces). A "normal" trajectory is also expected to

use the same timestep, frequency of saving frames, 4D-data, crystal data, fixed

atoms and fluctuating charges in all its individual files.

Trajectory files have to be opened, on consecutive unit numbers, before they

can be read:

open unform read unit 101 name traj1.trj

open unform read unit 102 name traj2.trj

open unform read unit 103 name traj3.trj

Negative numbers and units 5 and 6 cannot be used, and units in the approximate

range 90-99 are used internally by CHARMM. In FORTRAN 95/2003 there is no upper

limit defined for a unit number.

The trajectory is specified with these keywords:

FIRStunit int The unit number of the first file (101 in the example above)

NUNIts int The number of files (3 in the example)

BEGIn int The integration step number of the first frame to be used

STOP int The integration step number of the last frame to be used

SKIP int The number of integration steps to skip between frames to be read. If

the value given is not a multiple of the saving interval in the file,

CHARMM will try to use an appropriate value.

NOCHeck Disable all checks on file consistency. This allows multiple trajectory

files to be analyzed together even if they do not form a regular

time sequence of frames. BEGIn and STOP are not used in this case,

the files will be processed from beginning to end. If SKIP is specified

(>1) an attempt will be made to use every SKIP step in each file.

If SKIP is not specified, or if it is 1, all frames will be read.

Warnings and error messages will be printed when mismatches are

detected. BOMLev does not have to be changed.

Example. Assume that the three files traj1.trj, traj2.trj and traj3.trj were

created using the following dyanmics commands:

dyna start nstep 1000 nsavc 100 ! saves 10 frames (100, 200, ...1000)

dyna restart nstep 10000 nsavc 100 ! saves 100 frames (1100, 1200, ...10100)

dyna restart nstep 10000 nsavc 100 ! saves 100 frames (10200, 10300, ...20100)

To read every 500 stepes in the trajectory from step 5500 to 16000

the following specifiaction should be used (after the files have been opened as above):

FIRST 101 NUNIT 3 BEGIN 5500 SKIP 500 STOP 16000

[Syntax TRAJectory command]

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

There are four commands that comprise this facility.

1) Initializing trajectory I/O

TRAJectory {read-spec} {write-spec}

read-spec:== [FIRST unit] [NUNITint] [SKIP int]

[BEGIN INT] [STOP INT]

write-spec:== [IWRIte unit] [NWRIte int] [NFILE int] [EXPAnd] [VELOcity]

[NOTHer int] [DELTa real] [SKIP int]

FIRStunit (IREAd) - first unit to read from (default: do not read)

NUNIts (NREAd) - number of units to read from (default:1)

SKIP - skip value for both reading and writing (default:1)

IWRIte - first unit to write to (default: do not write)

NWRIte - number of units to write to (default:1)

NFILe - number of frames on each output file (default: total)

EXPAnd - flag to free fixed atoms in copying (only if reading)

VELOcity - flag to write velocity (default: coordinate)

NOTHer - number of frames in previous files (if not reading) (d:0)

DELTa - output delta value (if not reading) (default:0.001)

2) Reading a frame

TRAJectory READ [COMP]

The reading command does not have any specifiers other than

whether the comparison or main coordinates will be used.

3) Writing a frame

TRAJectory WRITe [COMP]

The writing command does not have any specifiers other than

whether the comparison or main coordinates will be used.

4) Query a trajectory file

TRAJectory QUERy UNIT integer

The query command rewinds an open trajectory file and then reads the

header information from this trajectory file. It prints a summary

and sets the following command line substitution parameters:

'NFILE' - Number of frames in the trajectory file

'START' - Step number for the first frame

'SKIP' - Frequency at which frames were saved

(NSTEP=NFILE*SKIP when not using restart files)

'NSTEP' - Total number of steps from the simulation

'NDEGF' - Number of degrees of freedom from the simulation

(Can be use to get the temperature with velocity files).

'DELTA' - The dynamics step length (in picoseconds).

This command, again, rewinds the trajectory file upon completion.

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

There are three modes of operation;

1) Create a new trajectory.

The IWRIte and NFILe keywords must be used. The default

values for the others are listed above. If several files

will be made in different CHARMM runs that will be linked together

later, the NOTHer keyword value should be increased by NFILe on

each subsequent run.

EXAMPLE: Create a "movie" trajectory that involves the rotation

of a single sidechain (residue 21).

COOR AXIS SELE ATOM * 21 CA END SELE ATOM * 21 CB

OPEN WRITE UNIT 22 FILE NAME TYR21.ROT

TRAJECTORY IWRITE 22 NWRITE 1 NFILE 360 SKIP 1

* trajectory showing the rotation of sidechain 21

SET 1 1

LABEL LOOP

COOR ROTATE AXIS PHI 1.0 SELE ATOM * 21 * .AND. .NOT. ( TYPE C -

.OR. TYPE N .OR. TYPE H ) END

TRAJ WRITE

INCR 1 BY 1

IF 1 LT 360.5 GOTO LOOP

STOP

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

2) Reading an existing trajectory

The FIRSTU (or IREAD) keyword must be used. The default NFILe value

is 1 and the remaining values if not specified will be read from the

trajectory file.

EXAMPLE: find the structure with the lowest energy and save it.

OPEN READ UNIT 22 FILE NAME DYN1.TRJ

OPEN READ UNIT 23 FILE NAME DYN2.TRJ

TRAJECTORY FIRSTU 22 NUNIT 2 SKIP 100

SET 1 1

SET 9 9999.0

CALC NTOT = ?NFILE * 2

LABEL LOOP

TRAJ READ

UPDATE ... ! depending on how much your atoms move,

! you may leave this outside the loop

GETE

IF 9 LT ?ENER GOTO NEXT

SET 8 @1

COOR COPY COMP

SET 9 ?ENER

LABEL NEXT

INCR 1 BY 1

IF 1 LT @NTOT GOTO LOOP

OPEN WRITE CARD UNIT 12 NAME LOWE.CRD

WRITE COOR COMP CARD UNIT 12

* structure with the lowest energy

* frame number @8 with energy @9

STOP

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

3) Copying from one trajectory to another.

The operation of this command works in the same mode as

the MERGE command, except a variety of CHARMM commands can

be executed between reading and writing of frames.

EXAMPLES: Create a new trajectory where every frame is minimized

for 200 steps.

OPEN READ UNIT 22 FILE NAME DYN.TRJ

OPEN WRITE UNIT 32 FILE NAME DYN.MIN

TRAJECTORY NUNIT 22 SKIP 100 IWRITE 32

* minimized trajectory

SET 1 1

LABEL LOOP

TRAJ READ

MINI ABNR NSTEP 200

TRAJ WRITE

INCR 1 BY 1

IF 1 LT ?NFILE GOTO LOOP

STOP

Reading and writing trajectory frames with direct commands

This facility allows the creation or manipulation of trajectory files

The main uses of this facility are;

1) creating artificial trajectory files from coordinate frames

2) reading an existing trajectory frame by frame for analysis that

requires access to a variety of CHARMM commands

3) modifying an existing trajectory (copy with changes) such as

minimizing each frame or other operations.

Handling trajectories stored in multiple files

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

All CHARMM commands and routines that can read trajectories use the same

syntax to specify how the trajectory should be read. For trajectories stored

in multiple files CHARMM checks that the files form a contiguous trajectory

(no overlaps or missing pieces). A "normal" trajectory is also expected to

use the same timestep, frequency of saving frames, 4D-data, crystal data, fixed

atoms and fluctuating charges in all its individual files.

Trajectory files have to be opened, on consecutive unit numbers, before they

can be read:

open unform read unit 101 name traj1.trj

open unform read unit 102 name traj2.trj

open unform read unit 103 name traj3.trj

Negative numbers and units 5 and 6 cannot be used, and units in the approximate

range 90-99 are used internally by CHARMM. In FORTRAN 95/2003 there is no upper

limit defined for a unit number.

The trajectory is specified with these keywords:

FIRStunit int The unit number of the first file (101 in the example above)

NUNIts int The number of files (3 in the example)

BEGIn int The integration step number of the first frame to be used

STOP int The integration step number of the last frame to be used

SKIP int The number of integration steps to skip between frames to be read. If

the value given is not a multiple of the saving interval in the file,

CHARMM will try to use an appropriate value.

NOCHeck Disable all checks on file consistency. This allows multiple trajectory

files to be analyzed together even if they do not form a regular

time sequence of frames. BEGIn and STOP are not used in this case,

the files will be processed from beginning to end. If SKIP is specified

(>1) an attempt will be made to use every SKIP step in each file.

If SKIP is not specified, or if it is 1, all frames will be read.

Warnings and error messages will be printed when mismatches are

detected. BOMLev does not have to be changed.

Example. Assume that the three files traj1.trj, traj2.trj and traj3.trj were

created using the following dyanmics commands:

dyna start nstep 1000 nsavc 100 ! saves 10 frames (100, 200, ...1000)

dyna restart nstep 10000 nsavc 100 ! saves 100 frames (1100, 1200, ...10100)

dyna restart nstep 10000 nsavc 100 ! saves 100 frames (10200, 10300, ...20100)

To read every 500 stepes in the trajectory from step 5500 to 16000

the following specifiaction should be used (after the files have been opened as above):

FIRST 101 NUNIT 3 BEGIN 5500 SKIP 500 STOP 16000

[Syntax TRAJectory command]

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

There are four commands that comprise this facility.

1) Initializing trajectory I/O

TRAJectory {read-spec} {write-spec}

read-spec:== [FIRST unit] [NUNITint] [SKIP int]

[BEGIN INT] [STOP INT]

write-spec:== [IWRIte unit] [NWRIte int] [NFILE int] [EXPAnd] [VELOcity]

[NOTHer int] [DELTa real] [SKIP int]

FIRStunit (IREAd) - first unit to read from (default: do not read)

NUNIts (NREAd) - number of units to read from (default:1)

SKIP - skip value for both reading and writing (default:1)

IWRIte - first unit to write to (default: do not write)

NWRIte - number of units to write to (default:1)

NFILe - number of frames on each output file (default: total)

EXPAnd - flag to free fixed atoms in copying (only if reading)

VELOcity - flag to write velocity (default: coordinate)

NOTHer - number of frames in previous files (if not reading) (d:0)

DELTa - output delta value (if not reading) (default:0.001)

2) Reading a frame

TRAJectory READ [COMP]

The reading command does not have any specifiers other than

whether the comparison or main coordinates will be used.

3) Writing a frame

TRAJectory WRITe [COMP]

The writing command does not have any specifiers other than

whether the comparison or main coordinates will be used.

4) Query a trajectory file

TRAJectory QUERy UNIT integer

The query command rewinds an open trajectory file and then reads the

header information from this trajectory file. It prints a summary

and sets the following command line substitution parameters:

'NFILE' - Number of frames in the trajectory file

'START' - Step number for the first frame

'SKIP' - Frequency at which frames were saved

(NSTEP=NFILE*SKIP when not using restart files)

'NSTEP' - Total number of steps from the simulation

'NDEGF' - Number of degrees of freedom from the simulation

(Can be use to get the temperature with velocity files).

'DELTA' - The dynamics step length (in picoseconds).

This command, again, rewinds the trajectory file upon completion.

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

There are three modes of operation;

1) Create a new trajectory.

The IWRIte and NFILe keywords must be used. The default

values for the others are listed above. If several files

will be made in different CHARMM runs that will be linked together

later, the NOTHer keyword value should be increased by NFILe on

each subsequent run.

EXAMPLE: Create a "movie" trajectory that involves the rotation

of a single sidechain (residue 21).

COOR AXIS SELE ATOM * 21 CA END SELE ATOM * 21 CB

OPEN WRITE UNIT 22 FILE NAME TYR21.ROT

TRAJECTORY IWRITE 22 NWRITE 1 NFILE 360 SKIP 1

* trajectory showing the rotation of sidechain 21

SET 1 1

LABEL LOOP

COOR ROTATE AXIS PHI 1.0 SELE ATOM * 21 * .AND. .NOT. ( TYPE C -

.OR. TYPE N .OR. TYPE H ) END

TRAJ WRITE

INCR 1 BY 1

IF 1 LT 360.5 GOTO LOOP

STOP

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

2) Reading an existing trajectory

The FIRSTU (or IREAD) keyword must be used. The default NFILe value

is 1 and the remaining values if not specified will be read from the

trajectory file.

EXAMPLE: find the structure with the lowest energy and save it.

OPEN READ UNIT 22 FILE NAME DYN1.TRJ

OPEN READ UNIT 23 FILE NAME DYN2.TRJ

TRAJECTORY FIRSTU 22 NUNIT 2 SKIP 100

SET 1 1

SET 9 9999.0

CALC NTOT = ?NFILE * 2

LABEL LOOP

TRAJ READ

UPDATE ... ! depending on how much your atoms move,

! you may leave this outside the loop

GETE

IF 9 LT ?ENER GOTO NEXT

SET 8 @1

COOR COPY COMP

SET 9 ?ENER

LABEL NEXT

INCR 1 BY 1

IF 1 LT @NTOT GOTO LOOP

OPEN WRITE CARD UNIT 12 NAME LOWE.CRD

WRITE COOR COMP CARD UNIT 12

* structure with the lowest energy

* frame number @8 with energy @9

STOP

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

3) Copying from one trajectory to another.

The operation of this command works in the same mode as

the MERGE command, except a variety of CHARMM commands can

be executed between reading and writing of frames.

EXAMPLES: Create a new trajectory where every frame is minimized

for 200 steps.

OPEN READ UNIT 22 FILE NAME DYN.TRJ

OPEN WRITE UNIT 32 FILE NAME DYN.MIN

TRAJECTORY NUNIT 22 SKIP 100 IWRITE 32

* minimized trajectory

SET 1 1

LABEL LOOP

TRAJ READ

MINI ABNR NSTEP 200

TRAJ WRITE

INCR 1 BY 1

IF 1 LT ?NFILE GOTO LOOP

STOP

Top

Merges or breaks up a trajectory into different numbers of files

Frequently, one generates a trajectory into small files to

minimize the CPU time of one job. However, so many files are usually

hard to manage so it is desirable to merge said files into larger units.

This command provides that capacity. In addition, it is possible to

break up the trajectory into smaller pieces and to sample the trajectory

less frequently than originally generated.

Another option is to optionally rotate the structure at each

frame to least squares fix a reference structure.

[Syntax MERGE dynamics trajectories]

MERGE [ COOR ] [FIRSTU unit-number] [NUNIT integer] [SKIP integer]

[ VEL ] [OUTPutu unit-number] [NFILE integer]

[ DRAW ] [BEGIN integer] [STOP integer]

[first-atom-selection]

[NOCRystal] [NOCHeck]

[ XFLUct ] [ UNFOld ]

[ ORIEnt [MASS] [WEIGht] [NOROt] [PRINT] second-atom-selection ]

[ RECEnter second-atom-selection] [ REPAck [IMAGes ] ]

[ SUBSset MEMSSU integer NUNSS integer ]

[ SIMPle ]

[ RTOTemp EXCU unit-number NEXChange integer NRPL integer NREPeat integer ]

Keyword table

Option Default Purpose

[COOR] COOR Specification of the type of trajectory file. COOR is

[VEL ] coordinates; VEL is velocities.

[DRAW] Make a CHARMM movie (do not write any files, just display)

FIRSTU 51 The first unit of the trajectory to be read.

NUNIT 1 The number of units to be read starting with FIRSTU

SKIP 1 Only those coordinate whose dynamics step number

modulo SKIP will be reoriented and written out.

OUTPUTU 61 The first unit number of the output trajectory

NFILE The number of coordinate sets written to each output

merged file. If left out, this will be set to the number

of coordinates in the first input file times the number of

input files. WARNING: This default will generate a bad

trajectory file if SKIP is not set to the interval

actually present in the trajectories. Further, if you

set its value to be larger than the number of

coordinates that are actually written in any output

file, you will have problems. The error that is

generated results from the control array in the

beginning specifying that there are more coordinates

than actually exist in the file. EOF errors will result

when the trajectory is read.

BEGIN First step number to start reading from

STOP Last step number to read

first-atom-sel Selection of atoms to include in the output file.

NOCRystal Suppress writing of crystal lattice data to output

trajectory if there is lattice data in input trajectory

and crystal facility has not been setup.

NOCHeck Do not check that input files are contiguous. Allows merging

of trajectory files from independent simulations. Output will

be to a single file, in which the steps will be numbered

1,2,3,... If SKIP > 1 an attempt will be made to use SKIP

when reading the input files.

NB! Header and crystal information in the output file may be

incorrect, and the file may be inappropriate for

timedependent analyses.

RECEnter Will re-center atoms based on the existing IMAGE

transformations ("coor ... rece ..") thus HAS to be

preceded by a normal image setup (read image, image

byresidue ..) for the atoms (usually solvent) that

are to be transformed as if the center of the primary

box coincided with the center of geometry of the

atoms in the second selection. In short: The second

selection defines the origin of your lattice

and the solvent molecules are put as close as possible to

the solute, even if things drifted slightly out of the box

during the simulation. Useful for calculation of solvation

properties. Does not work with XFLUct or UNFOld.

The possibly large amounts of output reporting on

all transformation operations being performed may

be suppressed by setting PRNLev 4, or PRNLev 1 to

get rid of the SELECTE IMAGES BEING CENTERED messages

as well.

NOTE: Uses SAME second-selection as ORIENt, so if

both RECEnter and ORIEnt are specified there should only

be one second selection, which will first be used

to define the recentering, then for the orienting.

REPAck Repacks the unit cell; by default, image transformations

are not used, and is therefore limited to orthogonal

unit cells with only translation operations. Intended

for use with DOMDEC simulations run w/o image centering.

Optional IMAGE keyword does standard image centering,

using the defined image centering point; this should *not*

be used to post-process uncentered DOMDEC trajectories.

Compatible with RECEnter and ORIEnt, and done first.

UNFOld removes the effects of image centering (not the same

as RECEnter), ie will let a particle continue out to

the right if that is what it was doing when PBC moved

it back into the primary box during the simulation.

XFLUct removes the effects of the box size/shape changes from

constant pressure simulations. This allows an accurate

calculation of transport properties (diffusion

constants,..) from CPT trajectories.

ORIEnt Flag to specify best fit rotation and translations.

MASS Use mass weighting in best fit.

WEIGht Use weighting array for best fit weights.

NOROt Only translate in the best fit.

PRINT Print the details of best fit

second-atom-sel Selection of atoms to use in the best fit.

NOTE: Uses SAME second-selection as RECEnter (see above)

RTOTemp Convert per-replica trajectories to per-temperature

trajectories (for use with FAST replica exchange as

described in repdstr.doc). If this option is selected,

NUNIT output files must be opened using consecutive

unit numbers starting with OUTU. FIRSTU is expected to

be the first of NUNIT consecutive unit numbers for each

of the per-replica trajectories in order from lowest to

highest. The following must also be given:

EXCU The unit number of the exchange file from FAST rep. exch.

NEXC The number of exchanges to process from EXCU.

NRPL Number of replicas.

NREP Number of repeats (set to 1 if not otherwise specified).

SIMPle Write the output in the simple trajectory format, suitable

for use as a reservoir in reservoir replica exchange (see

repdstr.doc for details). In this case, OUTU must be opened

for DIREct access.

SUBSET Creates up to 64 subset trajectory files from the input

trajectories (COOR only, no FIXed atoms), using a list

of subset members; the list file format is the same as

the membership list produced by the CLUSter command

within CORREL (see below). Additional keywords are:

MEMSSU Unit number for the subset membership list.

NUNSS Number of subset units, starting with OUTPUTU; the

unit numbers must be consecutive.

Additional notes on SUBSET:

(1) The time base is lost, as the output subset trajectory files are written

with SKIP 1 and a timestep of 1.0, for simple sequential numbering of frames.

(2) Each subset starts with BEGIN 1, and NFILE will be the number of members.

(3) Subsets w/o members are allowed; a file of zero length will be produced.

(4) ORIENT, UNFOLD, XFLUCT, and RECENTER are not allowed with SUBSET.

(5) The membership list file format is--

1 Cluster Membership File

3 Time Series Frames Clustered: 0, 720000

4 Maximum Cluster Radius : 0.9500E+02

5 Number of Patterns Clustered: 720001

6 Number of Clusters : 18

8 Cluster Frame 1stSeries Distance

9 12 0 1 0.7416E+02

: 8 1 1 0.3662E+02

8 2 1 0.4593E+02

8 3 1 0.4003E+02

8 4 1 0.3793E+02

: : : :

The first 8 lines must be present (but w/o the line numbers shown); lines

3-6 describe the data in lines 9+ (but the cluster radius is ignored). For

use with MERGE COOR SUBSET, only the first two data columns (Cluster, Frame)

are needed. Note that 'frame 0' will be ignored, as it is not present in

the trajectory files, but apparently represents the coordinates in MAIN when

the CLUSTER command was run.

For all MERGE operations, the title of the output trajectory will be

copied from the input trajectory.

Merges or breaks up a trajectory into different numbers of files

Frequently, one generates a trajectory into small files to

minimize the CPU time of one job. However, so many files are usually

hard to manage so it is desirable to merge said files into larger units.

This command provides that capacity. In addition, it is possible to

break up the trajectory into smaller pieces and to sample the trajectory

less frequently than originally generated.

Another option is to optionally rotate the structure at each

frame to least squares fix a reference structure.

[Syntax MERGE dynamics trajectories]

MERGE [ COOR ] [FIRSTU unit-number] [NUNIT integer] [SKIP integer]

[ VEL ] [OUTPutu unit-number] [NFILE integer]

[ DRAW ] [BEGIN integer] [STOP integer]

[first-atom-selection]

[NOCRystal] [NOCHeck]

[ XFLUct ] [ UNFOld ]

[ ORIEnt [MASS] [WEIGht] [NOROt] [PRINT] second-atom-selection ]

[ RECEnter second-atom-selection] [ REPAck [IMAGes ] ]

[ SUBSset MEMSSU integer NUNSS integer ]

[ SIMPle ]

[ RTOTemp EXCU unit-number NEXChange integer NRPL integer NREPeat integer ]

Keyword table

Option Default Purpose

[COOR] COOR Specification of the type of trajectory file. COOR is

[VEL ] coordinates; VEL is velocities.

[DRAW] Make a CHARMM movie (do not write any files, just display)

FIRSTU 51 The first unit of the trajectory to be read.

NUNIT 1 The number of units to be read starting with FIRSTU

SKIP 1 Only those coordinate whose dynamics step number

modulo SKIP will be reoriented and written out.

OUTPUTU 61 The first unit number of the output trajectory

NFILE The number of coordinate sets written to each output

merged file. If left out, this will be set to the number

of coordinates in the first input file times the number of

input files. WARNING: This default will generate a bad

trajectory file if SKIP is not set to the interval

actually present in the trajectories. Further, if you

set its value to be larger than the number of

coordinates that are actually written in any output

file, you will have problems. The error that is

generated results from the control array in the

beginning specifying that there are more coordinates

than actually exist in the file. EOF errors will result

when the trajectory is read.

BEGIN First step number to start reading from

STOP Last step number to read

first-atom-sel Selection of atoms to include in the output file.

NOCRystal Suppress writing of crystal lattice data to output

trajectory if there is lattice data in input trajectory

and crystal facility has not been setup.

NOCHeck Do not check that input files are contiguous. Allows merging

of trajectory files from independent simulations. Output will

be to a single file, in which the steps will be numbered

1,2,3,... If SKIP > 1 an attempt will be made to use SKIP

when reading the input files.

NB! Header and crystal information in the output file may be

incorrect, and the file may be inappropriate for

timedependent analyses.

RECEnter Will re-center atoms based on the existing IMAGE

transformations ("coor ... rece ..") thus HAS to be

preceded by a normal image setup (read image, image

byresidue ..) for the atoms (usually solvent) that

are to be transformed as if the center of the primary

box coincided with the center of geometry of the

atoms in the second selection. In short: The second

selection defines the origin of your lattice

and the solvent molecules are put as close as possible to

the solute, even if things drifted slightly out of the box

during the simulation. Useful for calculation of solvation

properties. Does not work with XFLUct or UNFOld.

The possibly large amounts of output reporting on

all transformation operations being performed may

be suppressed by setting PRNLev 4, or PRNLev 1 to

get rid of the SELECTE IMAGES BEING CENTERED messages

as well.

NOTE: Uses SAME second-selection as ORIENt, so if

both RECEnter and ORIEnt are specified there should only

be one second selection, which will first be used

to define the recentering, then for the orienting.

REPAck Repacks the unit cell; by default, image transformations

are not used, and is therefore limited to orthogonal

unit cells with only translation operations. Intended

for use with DOMDEC simulations run w/o image centering.

Optional IMAGE keyword does standard image centering,

using the defined image centering point; this should *not*

be used to post-process uncentered DOMDEC trajectories.

Compatible with RECEnter and ORIEnt, and done first.

UNFOld removes the effects of image centering (not the same

as RECEnter), ie will let a particle continue out to

the right if that is what it was doing when PBC moved

it back into the primary box during the simulation.

XFLUct removes the effects of the box size/shape changes from

constant pressure simulations. This allows an accurate

calculation of transport properties (diffusion

constants,..) from CPT trajectories.

ORIEnt Flag to specify best fit rotation and translations.

MASS Use mass weighting in best fit.

WEIGht Use weighting array for best fit weights.

NOROt Only translate in the best fit.

PRINT Print the details of best fit

second-atom-sel Selection of atoms to use in the best fit.

NOTE: Uses SAME second-selection as RECEnter (see above)

RTOTemp Convert per-replica trajectories to per-temperature

trajectories (for use with FAST replica exchange as

described in repdstr.doc). If this option is selected,

NUNIT output files must be opened using consecutive

unit numbers starting with OUTU. FIRSTU is expected to

be the first of NUNIT consecutive unit numbers for each

of the per-replica trajectories in order from lowest to

highest. The following must also be given:

EXCU The unit number of the exchange file from FAST rep. exch.

NEXC The number of exchanges to process from EXCU.

NRPL Number of replicas.

NREP Number of repeats (set to 1 if not otherwise specified).

SIMPle Write the output in the simple trajectory format, suitable

for use as a reservoir in reservoir replica exchange (see

repdstr.doc for details). In this case, OUTU must be opened

for DIREct access.

SUBSET Creates up to 64 subset trajectory files from the input

trajectories (COOR only, no FIXed atoms), using a list

of subset members; the list file format is the same as

the membership list produced by the CLUSter command

within CORREL (see below). Additional keywords are:

MEMSSU Unit number for the subset membership list.

NUNSS Number of subset units, starting with OUTPUTU; the

unit numbers must be consecutive.

Additional notes on SUBSET:

(1) The time base is lost, as the output subset trajectory files are written

with SKIP 1 and a timestep of 1.0, for simple sequential numbering of frames.

(2) Each subset starts with BEGIN 1, and NFILE will be the number of members.

(3) Subsets w/o members are allowed; a file of zero length will be produced.

(4) ORIENT, UNFOLD, XFLUCT, and RECENTER are not allowed with SUBSET.

(5) The membership list file format is--

1 Cluster Membership File

3 Time Series Frames Clustered: 0, 720000

4 Maximum Cluster Radius : 0.9500E+02

5 Number of Patterns Clustered: 720001

6 Number of Clusters : 18

8 Cluster Frame 1stSeries Distance

9 12 0 1 0.7416E+02

: 8 1 1 0.3662E+02

8 2 1 0.4593E+02

8 3 1 0.4003E+02

8 4 1 0.3793E+02

: : : :

The first 8 lines must be present (but w/o the line numbers shown); lines

3-6 describe the data in lines 9+ (but the cluster radius is ignored). For

use with MERGE COOR SUBSET, only the first two data columns (Cluster, Frame)

are needed. Note that 'frame 0' will be ignored, as it is not present in

the trajectory files, but apparently represents the coordinates in MAIN when

the CLUSTER command was run.

For all MERGE operations, the title of the output trajectory will be

copied from the input trajectory.

Top

Reorienting a coordinate trajectory

If one is interested in reorienting every set of coordinates

found in a dynamics trajectory with respect to some reference structure,

one can use the ORIEnt option in conjunction with the MERGe command.

The process of reorienting a coordinate trajectory works as

follows: A series of files containing the trajectory are assigned to

successive units prior to a CHARMM run. The coordinates stored therein

are presumed to have been written every NSAVC steps. CHARMM will read

each coordinate, select some periodically, reorient them, and write them

to successive units where each output file will have a user specified

number of coordinates. The following table lists the options involved:

Option Default Purpose

ORIE .false. Specify that a least squares RMS fit will be done.

MASS .false. Use a mass weighting in the fit

WEIGH .false. Use the weighting array (wmain) in the fit

NOROt .false. Just shift the centers to best fit.

PRINt .false. Print what happened to each coordinate set.

atom-selection all Select which atom to use in the fit.

If atoms were fixed during the dynamics, the new trajectory

produced will not have fixed atoms because the rotations applied to

each coordinate set will be different thereby yielding different

coordinates for the fixed atoms. Fixing the coordinates leads to a

large space reductions, so the reorientation process will therefore

result in potentially much larger trajectory files.

Reorienting a coordinate trajectory

If one is interested in reorienting every set of coordinates

found in a dynamics trajectory with respect to some reference structure,

one can use the ORIEnt option in conjunction with the MERGe command.

The process of reorienting a coordinate trajectory works as

follows: A series of files containing the trajectory are assigned to

successive units prior to a CHARMM run. The coordinates stored therein

are presumed to have been written every NSAVC steps. CHARMM will read

each coordinate, select some periodically, reorient them, and write them

to successive units where each output file will have a user specified

number of coordinates. The following table lists the options involved:

Option Default Purpose

ORIE .false. Specify that a least squares RMS fit will be done.

MASS .false. Use a mass weighting in the fit

WEIGH .false. Use the weighting array (wmain) in the fit

NOROt .false. Just shift the centers to best fit.

PRINt .false. Print what happened to each coordinate set.

atom-selection all Select which atom to use in the fit.

If atoms were fixed during the dynamics, the new trajectory

produced will not have fixed atoms because the rotations applied to

each coordinate set will be different thereby yielding different

coordinates for the fixed atoms. Fixing the coordinates leads to a

large space reductions, so the reorientation process will therefore

result in potentially much larger trajectory files.

**»**cons Fixed Atom.Top

Computes the RMS difference between two trajectory files

and make a matrix of results. Large files should be reduced with the

MERGe command before processing this command.

RMSDynamics ORIEnt [MASS] [WEIGht] [NOROt] [RMS|DRMS [atom-selection]]

[atom-selection]

FIRSTU unit-number [NUNIT integer]

BEGIN integer [SKIP integer] STOP integer [IWRIte unit-number]

[SECU unit-number] [BEG2 integer] [SKP2 integer] [STP2 integer]

( [IREAd unit-number] [JREAd unit-number])

([IMAGes]) [MATRix]

[PQUNit unit-number [PQSEed integer] [IOPT int] [MAXFn int] [NSIG int] ]

IWRIte int - Unit for the output matrix.

FIRSTu int - Unit number for first file containing trajectory 1

NUNIt int - Number of files for trajectory 1

BEGIn int - Starting step number

STOP int - Ending step number

SKIP int - Number of steps to skip (default 1)

NB! BEGIN, SKIP and STOP have to be specified to allow proper

memory allocation! The TRAJ QUERY command can retrieve these values

The trajectory(ies) are read into memory before calculations begin;

Memory usage may be reduced by decreasing the number of selected atoms,

and by reducing the number coordinate sets (frames) used - increase SKIP

SECU int

NUN2 int

BEG2 int Specifications for trajectory 2. Defaults to same values

SKP2 int as used for trajectory 1. If SECU is not given, or same as

STP2 int FIRStu only one trajectory will be analyzed.

(IREAd int - unit number of the first trajectory file.)

If only IREAd is specified, or if IREAd and JREAd are the same

the RMSDs will be between frames in same file

(JREAd int - unit number of the second trajectory file.)

NB! IREAD and JREAD are obsolete as of c30 (but still supported)

(IMAGes - Use image atoms for the analysis (not implemented))

ORIEnt - Do best fit of structures

MASS - Use a mass weighting in best fit.

WEIGht - Use the weighting array in best fit.

NOROt - Best fit without letting the structures rotate.

RMS - Do RMS fit between structures, otherwise,

align structures with the axis.

DRMS - Distance RMSD

For each frame, the RMS difference between interatomic

distances computed for the comparison coordinates and the

coordinates in the trajectory, using all atom pairs having

one atom in each selection. If no selection is given, all

atoms are used; if only one selection is given, all atom pairs

within this selection are used. If an atom i appears in both

selections the distance r(i)-r(i)=0 will not be included in

the calculation.

No other corrections are made wrt connectivity.

MATRix - output just the RMSDvalues in matrix format

NOTE: You have to specify correct BEGIN and STOP values so that

the correct amount of memory can be allocated

PQUNit int - unit number for output of (P,Q)-values in a 2D-projection of

the RSMD-map according to Levitt, M. J.Mol.Biol. (1983) 168,

621-657. CHARMM variable PQRES is set to the final value of

the target fcn. This can be slow to converge. PRNL 6

(or greater) outputs the value of the target fcn for each

iteration, allowing judgement of the convergence.

If iterations stop due to maximum number of function

evaluations reached, you can increase this with the MAXFn

<integer> keyword, and see if it results in a qualitative

change of the p{p,q}-pattern. If not all is probably OK.

The RMSD-values can be printed also when this option is on.

This turns on the MATRix flag so BEGIN and STOP have to be

correct. Requires the same number of frames to be used from boths

trajectories.

Uses IMSL-routine ZXMIN; IOPT,MAXFN and NSIG can be specified

to tune the behavior of ZXMIN.

PQSEed int - seed for random generation of initial guesses for the (P,Q).

prnl 6 gives a little more information about initial guesses

etc.

atom-selection

- Atoms to use in the fitting procedure, or in the DRMS calculation

Computes the RMS difference between two trajectory files

and make a matrix of results. Large files should be reduced with the

MERGe command before processing this command.

RMSDynamics ORIEnt [MASS] [WEIGht] [NOROt] [RMS|DRMS [atom-selection]]

[atom-selection]

FIRSTU unit-number [NUNIT integer]

BEGIN integer [SKIP integer] STOP integer [IWRIte unit-number]

[SECU unit-number] [BEG2 integer] [SKP2 integer] [STP2 integer]

( [IREAd unit-number] [JREAd unit-number])

([IMAGes]) [MATRix]

[PQUNit unit-number [PQSEed integer] [IOPT int] [MAXFn int] [NSIG int] ]

IWRIte int - Unit for the output matrix.

FIRSTu int - Unit number for first file containing trajectory 1

NUNIt int - Number of files for trajectory 1

BEGIn int - Starting step number

STOP int - Ending step number

SKIP int - Number of steps to skip (default 1)

NB! BEGIN, SKIP and STOP have to be specified to allow proper

memory allocation! The TRAJ QUERY command can retrieve these values

The trajectory(ies) are read into memory before calculations begin;

Memory usage may be reduced by decreasing the number of selected atoms,

and by reducing the number coordinate sets (frames) used - increase SKIP

SECU int

NUN2 int

BEG2 int Specifications for trajectory 2. Defaults to same values

SKP2 int as used for trajectory 1. If SECU is not given, or same as

STP2 int FIRStu only one trajectory will be analyzed.

(IREAd int - unit number of the first trajectory file.)

If only IREAd is specified, or if IREAd and JREAd are the same

the RMSDs will be between frames in same file

(JREAd int - unit number of the second trajectory file.)

NB! IREAD and JREAD are obsolete as of c30 (but still supported)

(IMAGes - Use image atoms for the analysis (not implemented))

ORIEnt - Do best fit of structures

MASS - Use a mass weighting in best fit.

WEIGht - Use the weighting array in best fit.

NOROt - Best fit without letting the structures rotate.

RMS - Do RMS fit between structures, otherwise,

align structures with the axis.

DRMS - Distance RMSD

For each frame, the RMS difference between interatomic

distances computed for the comparison coordinates and the

coordinates in the trajectory, using all atom pairs having

one atom in each selection. If no selection is given, all

atoms are used; if only one selection is given, all atom pairs

within this selection are used. If an atom i appears in both

selections the distance r(i)-r(i)=0 will not be included in

the calculation.

No other corrections are made wrt connectivity.

MATRix - output just the RMSDvalues in matrix format

NOTE: You have to specify correct BEGIN and STOP values so that

the correct amount of memory can be allocated

PQUNit int - unit number for output of (P,Q)-values in a 2D-projection of

the RSMD-map according to Levitt, M. J.Mol.Biol. (1983) 168,

621-657. CHARMM variable PQRES is set to the final value of

the target fcn. This can be slow to converge. PRNL 6

(or greater) outputs the value of the target fcn for each

iteration, allowing judgement of the convergence.

If iterations stop due to maximum number of function

evaluations reached, you can increase this with the MAXFn

<integer> keyword, and see if it results in a qualitative

change of the p{p,q}-pattern. If not all is probably OK.

The RMSD-values can be printed also when this option is on.

This turns on the MATRix flag so BEGIN and STOP have to be

correct. Requires the same number of frames to be used from boths

trajectories.

Uses IMSL-routine ZXMIN; IOPT,MAXFN and NSIG can be specified

to tune the behavior of ZXMIN.

PQSEed int - seed for random generation of initial guesses for the (P,Q).

prnl 6 gives a little more information about initial guesses

etc.

atom-selection

- Atoms to use in the fitting procedure, or in the DRMS calculation

Top

Format or unformat a dynamics trajectory

DYNAmics FORMat FIRStunit <unit> NUNIt <int> BEGIn <int>

SKIP <int> STOP <int> OUTPut <unit>

OFFSet <int> SCALe <int> MODE <FORTRAN-FORMAT>

DYNAmics UNFOrmat INPUt <unit> OUTPut <unit>

These commands allow to convert binary trajectory files into a machine

independent yet compact format and to convert them back into binary files.

The defaults for OFFSet, SCALe and MODE are: OFFSet=600, SCALE=10000, and

MODE=12Z6. The trajectory is converted into positive integers according to

the formula <integer>=INT(<real>+OFFSET)*SCALE). The user has to make

sure that all coordinates of the trajectory are within OFFSET angstroms.

The precision may be increased by choosing a larger SCALE and FORTRAN-format,

e.g. MODE=11Z7 OFFSET=100000. ("Z" is the hexadecimal format and is available

on most machines.)

Format or unformat a dynamics trajectory

DYNAmics FORMat FIRStunit <unit> NUNIt <int> BEGIn <int>

SKIP <int> STOP <int> OUTPut <unit>

OFFSet <int> SCALe <int> MODE <FORTRAN-FORMAT>

DYNAmics UNFOrmat INPUt <unit> OUTPut <unit>

These commands allow to convert binary trajectory files into a machine

independent yet compact format and to convert them back into binary files.

The defaults for OFFSet, SCALe and MODE are: OFFSet=600, SCALE=10000, and

MODE=12Z6. The trajectory is converted into positive integers according to

the formula <integer>=INT(<real>+OFFSET)*SCALE). The user has to make

sure that all coordinates of the trajectory are within OFFSET angstroms.

The precision may be increased by choosing a larger SCALE and FORTRAN-format,

e.g. MODE=11Z7 OFFSET=100000. ("Z" is the hexadecimal format and is available

on most machines.)

Top

CONSTANT VELOCITY

The code for constant velocity was generalized in c34a1 code. Use

single selection in CVELocity command. The comparison set is used for

the refernce structure. When two selections are scpecified the

folowing still works:

A constant velocity method has been developed for use with DYNA (right

now, it only works with LEAP [in charmm] and LOBATTO [in MBO(N)D] integrators).

The main purpose of this facility is to run simulations similar to atomic force

microscopy. The constant velocity method, therefore, is used in

conjunction with the NOE facility used to apply a 'spring' between two

atoms.

A constant velocity for an atom is entered via CVEL in CHARMM syntax:

CVELocity <real> <sele first atom> <sele second atom>

where <real> = constant velocity in Angst/ps; the constant velocity vector

and direction is defined from <sele first atom> to <sele second atom>. the

position of the <sele second atom>, typically a dummy atom, is moved to

the position of <sele first atom> + 0.0001 Angstr. along the vector

(because charmm does not like duplicate coordinates); <sele second atom>

then traverses along the vector at the constant velocity rate.

The second atom is not really needed, but it is helpful in analyzing

the vector visually before running dynamics.

Note: If you want to apply a spring between the constant velocity atom

and the first atom in the vector, you must use (currently) the NOE facility

in charmm.

---

Here are the relavent syntax from a sample input file (typical usage).

---

*afm.inp

*Simulated Atomic Force Microscopy

*Continually loops over 10ps segments of dynamics (NVT'ish)

...lots of typical charmm stufff...

!--------DEFINITIONS

!Two atoms, one is the near the end of myosin, the other is a dummy atom

! to be cvel'ed

define tip SELE atom dumm 1 dumm END

define pp SELE atom hc 835 ca END

!Actin binding region

define actb sele segid hc .and. (resi 405:415 .or. resi 529:550 .or. -

resi 626:647) end

!----FORCES

set f 4. !spring constant; See Grubmueller Science 1996, 271, 997

set com 100 !force used to pin actin binding site

set max 80 !tot number of dyn runs--arbitrary right now

!##CVEL <Angst/ps> <first_single_atom_selec> <second_single_atom_selec>

!## These two atoms define the pulling vector; the first selection

!## is the pull point, and the second selection is the atom that moves at

!## constant velocity along the pull point. Currently, the 'spring'

!## between these two atoms is defined using the NOE facility below.

cvel @{cv} SELE pp END SELE tip END

!set up spring between atoms in cvel

noe

reset

assign SELE pp END SELE tip END -

kmin 0.0 rmin 0.0 kmax @f rmax .00001 fmax 1000

PRINT ANAL

end

label skip

!----Pin protein

cons harm sele actb end force @{com}

DYNAMICS MBOND (or LEAP) (re)START -

dynamics equilibration or constant temperature method.

!lots of loops over the above

stop

References:

1. Grubmueller Science 1996, 271, 997.

2. "The Evaluation Of Multi-Body Dynamics For Studying Ligand-Protein

Interactions. Using MBO(N)D To Probe The Unbinding Pathways Of

Cbz-Val-Phe-Phe-Val-Cbz From The Active Site Of Hiv-1 Protease" Chin, D.

N.; Haney, D. N.; Delak, K.; Chun, H. M.; Padilla, C, In Rational Drug

Design; Parrill, A., Reddy, R. Eds.; ACS Washington, 1998, in press.

MODIFIED CODE IN CHARMM 26??

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

a build/sgi/newmk/charmm.mk 9 blocks

a build/sgi/newmk/dynamc.mk 25 blocks

a build/sgi/newmk/mbond.mk 17 blocks

a source/fcm/newfcm/cveloci.fcm 2 blocks

a source/dynamc/newsrc/cveloci.src 9 blocks

a source/dynamc/newsrc/dcntrl.src 110 blocks

a source/dynamc/newsrc/dynamc.src 104 blocks

a source/charmm/newsrc/charmm_main.src 47 blocks

a source/charmm/newsrc/iniall.src 57 blocks

a source/moldyn/newsrc/compin.f 24 blocks

a source/moldyn/newsrc/delta_v.f 19 blocks

a source/moldyn/newsrc/engmom.f 21 blocks

a source/moldyn/newsrc/engmom_ke.f 9 blocks

a source/moldyn/newsrc/mbdyna.f 58 blocks

a source/moldyn/newsrc/ydot.f 74 blocks

a source/moldyn/newsrc/CHARMM.INC

a source/mbond/newsrc/mbback.src 52 blocks

a source/mbond/newsrc/mbdyn.src 40 blocks

CONSTANT VELOCITY

The code for constant velocity was generalized in c34a1 code. Use

single selection in CVELocity command. The comparison set is used for

the refernce structure. When two selections are scpecified the

folowing still works:

A constant velocity method has been developed for use with DYNA (right

now, it only works with LEAP [in charmm] and LOBATTO [in MBO(N)D] integrators).

The main purpose of this facility is to run simulations similar to atomic force

microscopy. The constant velocity method, therefore, is used in

conjunction with the NOE facility used to apply a 'spring' between two

atoms.

A constant velocity for an atom is entered via CVEL in CHARMM syntax:

CVELocity <real> <sele first atom> <sele second atom>

where <real> = constant velocity in Angst/ps; the constant velocity vector

and direction is defined from <sele first atom> to <sele second atom>. the

position of the <sele second atom>, typically a dummy atom, is moved to

the position of <sele first atom> + 0.0001 Angstr. along the vector

(because charmm does not like duplicate coordinates); <sele second atom>

then traverses along the vector at the constant velocity rate.

The second atom is not really needed, but it is helpful in analyzing

the vector visually before running dynamics.

Note: If you want to apply a spring between the constant velocity atom

and the first atom in the vector, you must use (currently) the NOE facility

in charmm.

---

Here are the relavent syntax from a sample input file (typical usage).

---

*afm.inp

*Simulated Atomic Force Microscopy

*Continually loops over 10ps segments of dynamics (NVT'ish)

...lots of typical charmm stufff...

!--------DEFINITIONS

!Two atoms, one is the near the end of myosin, the other is a dummy atom

! to be cvel'ed

define tip SELE atom dumm 1 dumm END

define pp SELE atom hc 835 ca END

!Actin binding region

define actb sele segid hc .and. (resi 405:415 .or. resi 529:550 .or. -

resi 626:647) end

!----FORCES

set f 4. !spring constant; See Grubmueller Science 1996, 271, 997

set com 100 !force used to pin actin binding site

set max 80 !tot number of dyn runs--arbitrary right now

!##CVEL <Angst/ps> <first_single_atom_selec> <second_single_atom_selec>

!## These two atoms define the pulling vector; the first selection

!## is the pull point, and the second selection is the atom that moves at

!## constant velocity along the pull point. Currently, the 'spring'

!## between these two atoms is defined using the NOE facility below.

cvel @{cv} SELE pp END SELE tip END

!set up spring between atoms in cvel

noe

reset

assign SELE pp END SELE tip END -

kmin 0.0 rmin 0.0 kmax @f rmax .00001 fmax 1000

PRINT ANAL

end

label skip

!----Pin protein

cons harm sele actb end force @{com}

DYNAMICS MBOND (or LEAP) (re)START -

dynamics equilibration or constant temperature method.

!lots of loops over the above

stop

References:

1. Grubmueller Science 1996, 271, 997.

2. "The Evaluation Of Multi-Body Dynamics For Studying Ligand-Protein

Interactions. Using MBO(N)D To Probe The Unbinding Pathways Of

Cbz-Val-Phe-Phe-Val-Cbz From The Active Site Of Hiv-1 Protease" Chin, D.

N.; Haney, D. N.; Delak, K.; Chun, H. M.; Padilla, C, In Rational Drug

Design; Parrill, A., Reddy, R. Eds.; ACS Washington, 1998, in press.

MODIFIED CODE IN CHARMM 26??

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

a build/sgi/newmk/charmm.mk 9 blocks

a build/sgi/newmk/dynamc.mk 25 blocks

a build/sgi/newmk/mbond.mk 17 blocks

a source/fcm/newfcm/cveloci.fcm 2 blocks

a source/dynamc/newsrc/cveloci.src 9 blocks

a source/dynamc/newsrc/dcntrl.src 110 blocks

a source/dynamc/newsrc/dynamc.src 104 blocks

a source/charmm/newsrc/charmm_main.src 47 blocks

a source/charmm/newsrc/iniall.src 57 blocks

a source/moldyn/newsrc/compin.f 24 blocks

a source/moldyn/newsrc/delta_v.f 19 blocks

a source/moldyn/newsrc/engmom.f 21 blocks

a source/moldyn/newsrc/engmom_ke.f 9 blocks

a source/moldyn/newsrc/mbdyna.f 58 blocks

a source/moldyn/newsrc/ydot.f 74 blocks

a source/moldyn/newsrc/CHARMM.INC

a source/mbond/newsrc/mbback.src 52 blocks

a source/mbond/newsrc/mbdyn.src 40 blocks

Top

Molecular Dynamics in the Tsallis (Generalized) Ensemble

Molecular dynamics that yield averages for a Tsallis (generalized) ensemble

rather than a canonical one can now be performed. At present, this method

is implemented only for the leapfrog Verlet integrator (dynamc.src); the

TSALLIS keyword must be included in pref.dat when compiling. The method is

invoked by adding to the DYNAmics command the keywords:

TSALlis QTSAllis real EMIN real

where QTSAllis is the Tsallis q and EMIN is the estimated minimum energy

of the system. The default value of QTSAllis is 1, in which case the

method reduces to standard (canonical) dynamics. Values of q larger than

1 effectively correspond to a smoothed potential in which the positions of

the extrema are preserved. Estimates for EMIN should err lower than any

possible energy of the system encountered during the simulation.

It is important to note that the scale factor for the forces involves

a temperature. The temperature employed in the Tsallis transformation

corresponds to the one used to assign the velocities during heating and

equilibration (TSTRUC initially and then FIRSTT + int*TEMINC). Thus, it

is important to set FIRSTT, FINALT and TEMINC appropriately even if one

is running Langevin dynamics at temperature TBATh (i.e., for equilibrium

dynamics, set FIRSTT = FINALT = TBATh).

Reference:

Andricioaei, I. and Straub, J. E. (1997) On Monte Carlo and molecular dynamics

methods inspired by Tsallis statistics: Methodology, optimization, and

application to atomic clusters. J. Chem. Phys. 107, 9117-9124.

Molecular dynamics with Tsallis scaling of the CMAP and dihedral

potential energy terms

Molecular dynamics using Tsallis scaling of the CMAP and Dihedral potential

terms can now be performed. This method is implemented for all integrators

(dynamc.src). In additional, the Tsallis scaling of the total potential

energy is implemented for VV2 (dynamvv2.src) and VV (dynamvv.src) integrators.

The method for Tsallis scaling of the CMAP and Dihedral potential

terms is invoked by adding to the DYNAmics command the keywords:

TTSALlis QTSAllis real EMIN real

where QTSAllis is the Tsallis q and EMIN is the estimated minimum energy

of the CMAP + Dihedral terms, having similar meaning as for TSALLIS. The

default value of QTSAllis is 1, in which case the method reduces to

standard dynamics (no scaling). Values of q larger than 1 effectively

correspond to a smoothed potential in which the positions of the extrema are

preserved. Estimates for EMIN should be lower than any possible energy of

the CMAP+Dihedral potential terms encountered during the simulation.

It is important to note that the scale factor for the forces involves a

temperature. The temperature employed in the Tsallis transformation

corresponds to the one used to assign the velocities during heating and

equilibration (TSTRUC initially and then FIRSTT + int*TEMINC). Thus, it is

important to set FIRSTT, FINALT and TEMINC appropriately even if one is

running Langevin dynamics at temperature TBATh (i.e., for equilibrium

dynamics, set FIRSTT = FINALT = TBATh).

Furthermore, simple scaling of the CMAP and Dihedral potential terms can also

be performed by adding to the DYNAmics command the keywords:

POTSaling TSALpha

where TSALpha is the scaling factor of the CMAP + Dihedral terms.

The default value of TSALpha is 1, in which case the method reduces to

standard dynamics (no scaling). Values of Alpha smaller than 1 correspond

to a smoothed potential.

Reference:

H. Kamberaj and A. van der Vaart (2007) Multiple Scaling Replica Exchange

for the Conformational Sampling of Biomolecules in Explicit Water.

J. Chem. Phys., 127, 234102-7.

Molecular Dynamics in the Tsallis (Generalized) Ensemble

Molecular dynamics that yield averages for a Tsallis (generalized) ensemble

rather than a canonical one can now be performed. At present, this method

is implemented only for the leapfrog Verlet integrator (dynamc.src); the

TSALLIS keyword must be included in pref.dat when compiling. The method is

invoked by adding to the DYNAmics command the keywords:

TSALlis QTSAllis real EMIN real

where QTSAllis is the Tsallis q and EMIN is the estimated minimum energy

of the system. The default value of QTSAllis is 1, in which case the

method reduces to standard (canonical) dynamics. Values of q larger than

1 effectively correspond to a smoothed potential in which the positions of

the extrema are preserved. Estimates for EMIN should err lower than any

possible energy of the system encountered during the simulation.

It is important to note that the scale factor for the forces involves

a temperature. The temperature employed in the Tsallis transformation

corresponds to the one used to assign the velocities during heating and

equilibration (TSTRUC initially and then FIRSTT + int*TEMINC). Thus, it

is important to set FIRSTT, FINALT and TEMINC appropriately even if one

is running Langevin dynamics at temperature TBATh (i.e., for equilibrium

dynamics, set FIRSTT = FINALT = TBATh).

Reference:

Andricioaei, I. and Straub, J. E. (1997) On Monte Carlo and molecular dynamics

methods inspired by Tsallis statistics: Methodology, optimization, and

application to atomic clusters. J. Chem. Phys. 107, 9117-9124.

Molecular dynamics with Tsallis scaling of the CMAP and dihedral

potential energy terms

Molecular dynamics using Tsallis scaling of the CMAP and Dihedral potential

terms can now be performed. This method is implemented for all integrators

(dynamc.src). In additional, the Tsallis scaling of the total potential

energy is implemented for VV2 (dynamvv2.src) and VV (dynamvv.src) integrators.

The method for Tsallis scaling of the CMAP and Dihedral potential

terms is invoked by adding to the DYNAmics command the keywords:

TTSALlis QTSAllis real EMIN real

where QTSAllis is the Tsallis q and EMIN is the estimated minimum energy

of the CMAP + Dihedral terms, having similar meaning as for TSALLIS. The

default value of QTSAllis is 1, in which case the method reduces to

standard dynamics (no scaling). Values of q larger than 1 effectively

correspond to a smoothed potential in which the positions of the extrema are

preserved. Estimates for EMIN should be lower than any possible energy of

the CMAP+Dihedral potential terms encountered during the simulation.

It is important to note that the scale factor for the forces involves a

temperature. The temperature employed in the Tsallis transformation

corresponds to the one used to assign the velocities during heating and

equilibration (TSTRUC initially and then FIRSTT + int*TEMINC). Thus, it is

important to set FIRSTT, FINALT and TEMINC appropriately even if one is

running Langevin dynamics at temperature TBATh (i.e., for equilibrium

dynamics, set FIRSTT = FINALT = TBATh).

Furthermore, simple scaling of the CMAP and Dihedral potential terms can also

be performed by adding to the DYNAmics command the keywords:

POTSaling TSALpha

where TSALpha is the scaling factor of the CMAP + Dihedral terms.

The default value of TSALpha is 1, in which case the method reduces to

standard dynamics (no scaling). Values of Alpha smaller than 1 correspond

to a smoothed potential.

Reference:

H. Kamberaj and A. van der Vaart (2007) Multiple Scaling Replica Exchange

for the Conformational Sampling of Biomolecules in Explicit Water.

J. Chem. Phys., 127, 234102-7.

Top

Description of the CENT Command

[ CENT NCRES int ]

Description: The reCENTering command allows to recenter the system

at the geometric center of the first NCRES residues in the psf file.

This keyword is useful when modelling a protein/water system using the

periodic boundary conditions to prevent the protein from driffting

outside of the primary unit cell. It can be replaced by the IMAGe keyword

when the solute is a small organic molecule.

Syntaxis: The Keyword CENT, which is specified in the DYNAmics command

line, turns on the recentering option for the system at the start of

a dynamics calculation (dcntrl.src) and at each update of the

nonbonded list (heuristic.src)

NCRES int - The first N (int) residues in the psf file,

based on which the system will be centered.

Description of the CENT Command

[ CENT NCRES int ]

Description: The reCENTering command allows to recenter the system

at the geometric center of the first NCRES residues in the psf file.

This keyword is useful when modelling a protein/water system using the

periodic boundary conditions to prevent the protein from driffting

outside of the primary unit cell. It can be replaced by the IMAGe keyword

when the solute is a small organic molecule.

Syntaxis: The Keyword CENT, which is specified in the DYNAmics command

line, turns on the recentering option for the system at the start of

a dynamics calculation (dcntrl.src) and at each update of the

nonbonded list (heuristic.src)

NCRES int - The first N (int) residues in the psf file,

based on which the system will be centered.