Syntax of the Dynamics Verlet Statement

The dynamics Verlet statement sets up various parameters for molecular dynamics as well as Langevin dynamics and then executes the specified number of steps.

DYNAmics VERLet

{ $<$dynamics-Verlet-statement$>$ } END is invoked from the main level of X-PLOR.

$<$dynamics-Verlet-statement$>$ :==

ASCIi=$<$logical$>$

writes a formatted (ASCII) coordinate trajectory file if ASCIi is TRUE; if ASCIi is FALSE, writes an unformatted (binary) file. In the former case, a scale factor $s$ and an offset $o$ are applied to the coordinates $r$ (i.e., $r'=s*(r+o)$); the result is converted to an integer number and written to the ASCII file using the specified format. If a hexadecimal format is specified, care should be taken to ensure that the application of the scale factor $s$ and the offset $o$ results in positive coordinates during the whole course of the molecular dynamics simulation. Otherwise, FORTRAN format runtime errors will occur.

CSEL=$<$selection$>$

selects atoms that are written to the coordinate trajectory file (default: all atoms except those fixed by the constraints fix statement).

FINAltemp=$<$real$>$

determines the target temperature for the velocity rescaling option (see ISCVel) (default: 298K).

FIRSttemp=$<$real$>$

assigns the temperature that determines the initial velocity (default: 0K).

FORMat=$<$string$>$

provides FORTRAN format for the ASCIi= TRUE option (default: 12Z.6, hexadecimal).

IASVelocity=$<$MAXWell$\vert$UNIForm$\vert$CURRent$>$

determines the
mode of initial velocity assignments (default: zero velocities).

IEQFrq=$<$integer$>$

determines the frequency with which the velocities are rescaled (default: 0). It works in conjunction with FINAltemperature.

ILBFrq=$<$integer$>$

updates Langevin boundary between normal and Langevin particles (default: 0). It works in conjunction with RBUF and ORIGin.

IPRFrq=$<$integer$>$

prints energy statistics every IPRFrq steps if not equal to zero (default: 50).

ISCVel=$<$integer$>$

determines the velocity rescale mode (default: 0).

ISVFrq=$<$integer$>$

determines how often a restart file is written to disk (default: 0).

NPRInt=$<$integer$>$

determines the frequency with which the energy is printed to standard output (default: 1, i.e., at every dynamics step).

NSAVC=$<$integer$>$

determines the frequency with which the coordinates are written to the coordinate trajectory file (default: 0).

NSAVV=$<$integer$>$

determines the frequency with which the velocities are written to the velocity trajectory file (default: 0).

NSTEp=$<$integer$>$

determines the number of steps. In the case of a restart, the steps executed before writing the restart file are included in NSTEP (e.g., if NSTEP=3000, but 1000 steps were run before writing the restart file, the program will execute only 2000 steps) (default: 100).

NTRFrq=$<$integer$>$

determines the frequency with which the center-of-mass motion is removed (default: 0).

OFFSet=$<$real$>$

provides offset $o$ for the ASCIi=TRUE option (default: 800).

ORIGin=$<$vector$>$

is the origin of the sphere of the Langevin boundary (default: 0,0,0).

RBUF=$<$real$>$

specifies the radius of the spherical boundary in a dynamics Verlet statement. Inside the boundary, the particles are “normal" molecular dynamics particles; outside they are propagated as Langevin particles (default: 0).

RESTart=filename

reads restart information from the named file and restarts the dynamics (default: no restart).

SAVE=$<$filename$>$

specifies the name of the file to which the program periodically writes the restart information (default: none).

SCALe=$<$real$>$

provides a scale factor $s$ for the ASCIi=TRUE option (default: 10000).

TBATh=$<$real$>$

specifies the temperature of the heatbath or the target temperature of Berendsen's temperature-coupling method.

TCOUpling=$<$logical$>$

is a logical flag that turns on Berendsen's temperature-coupling method. This flag works in conjunction with TBATh (default: FALSE).

TIMEstep=$<$real$>$

assigns the time step $\Delta t$ value for the finite-difference integration in psec (default: 0.001 psec).

TRAJectory=$<$file$>$

provides the filename of the coordinate trajectory file (default: none).

VASCii=$<$logical$>$

writes a formatted (ASCII) velocity trajectory file if VASCii is TRUE; if VASCii is FALSE, an unformatted (binary) velocity trajectory file is written. In the former case, a scale factor $s$ and an offset $o$ are applied to the velocities $r$ (i.e., $r'=s_v*(r+o_v)$); the result is converted to an integer number and written to the ASCII file using the specified format. If a hexadecimal format is specified, care should be taken to ensure that the application of the scale factor $s_v$ and the offset $o_v$ results in positive velocities during the whole course of the molecular dynamics simulation. Otherwise, FORTRAN format runtime errors will occur.

VELOcity=$<$filename$>$

names the velocity trajectory file (default: none).

VFORmat=$<$string$>$

is the FORTRAN format of the velocity trajectory file for the VASCii= TRUE option (default: 12Z.6, hexadecimal).

VOFFset=$<$real$>$

provides an offset $o_v$ for the VASCii= TRUE option (default: 300).

VSCAle=$<$real$>$

provides a scale factor $s_v$ for the VASCii=TRUE option (default: 10000).

VSEL=$<$selection$>$

selects atoms that are written to the velocity trajectory file (default: all atoms except those fixed by the constraints fix statement).