Syntax of the Dynamics Rigid Statement

This statement sets up various parameters for rigid-body dynamics and then executes the specified number of dynamics steps. Parts of the molecule that are not specified in any GROUp statement will remain fixed. The constraints fix statement (Section 8.1) has no influence on rigid-body molecular dynamics (except for the default group selection).

DYNAmics RIGId

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

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

ASCIi=$<$logical$>$

writes a formatted (ASCII) coordinate trajectory file if ASCIi is TRUE; if ASCIi is FALSE, an unformatted (binary) file is written. 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).

DT=$<$real$>$

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

DYNMODE=$<$string$>$

selects from three possible rigid-body dynamics modes: FREE, LANGevin, or TCOUpling (default: FREE).

FORMat=$<$string$>$

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

GROUp=$<$selection$>$

selects atoms that will form a rigid group. Multiple specification of GROUps will define multiple rigid groups. The group selections have to be disjoint (default: one group consisting of all atoms except those that have been fixed by the constraints fix statement; the default is overwritten as soon as a GROUp statement is issued).

NPRInt=$<$integer$>$

determines the frequency with which the energy is printed in 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 (default: 100).

NTRFrq=$<$integer$>$

determines the update frequency to remove the overall center-of-mass translation and rotation of all “free" atoms (default: 0).

OFFSet=$<$real$>$

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

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 the temperature-coupling method.

TCOUpling=$<$logical$>$

denotes the Berendsen temperature-coupling method, which works in conjunction with TBATh (default: FALSE).

TRAJectory=$<$file$>$

names 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=$<$file$>$

names the velocity trajectory file (default: none).

VFORmat=$<$string$>$

is the FORTRAN format of 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).