dynamc (c46b2)

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). See » 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. See » tpcontrol Dynamics.

In order to generate a dynamics trajectory, all requirements
for evaluating the energy must be met.
See » 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
* pressure: CPT dynamics
* sgld: Self-guided molecular/Langevin dynamics
* fourd: 4-D dynamics
* pressure: Pressure. The pressure command
* mts: Multiple Time Scales Method
* nose: Nose-Hoover Dynamics
* mbond: Dynamic. Multi-body Dynamics


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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::= See » hbonds
nonbond-spec::= See » nbonds
mbond-spec::= See » mbond DynDesc.
sgmd-sgld-spec::= See » sgld
domdec-spec::= See » domdec
openmm-spec::= See » 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::= See » pressure

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]


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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 See » nbonds

hbond- The specifications for generating the hydrogen bond list.
-spec See » 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. » random

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.
See » mbond DynDesc for a
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.


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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,
see » cons SHAKE. SHAKE can be applied to just
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, see » cons fixed atom. If this
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.


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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


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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


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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.info). 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.info 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.


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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.
See » cons Fixed Atom.


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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


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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.)

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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


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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.


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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.