U.S. flag

An official website of the United States government
  next up previous contents index  Xplor-NIH home Documentation

Next: Requirements Up: Merging Trajectories Previous: Merging Trajectories


Syntax

DYNAmics MERGe
{ $<$dynamics-merge-statement$>$ } END is invoked from the main level of X-PLOR
$<$dynamics-merge-statement$>$ :==
$<$trajectory-statement$>$
is defined in Section 12.1.3.
ENSEmble=$<$logical$>$
for ENSEmble=TRUE bypasses the mismatch checking between subsequent trajectory files. In this way it is possible to generate a pseudotrajectory from a group of otherwise unrelated trajectory files for the same system. One example where this option is useful consists of the merging of several independent molecular dynamics simulations in order to compute time-independent properties.
FORMat=$<$string$>$
is the FORTRAN format for the OASCii=TRUE option. If the hexadecimal format is specified when writing an ASCII trajectory file, care should be taken to ensure that the coordinates after application of the scale factor $s$ and the offset $o$ are all positive during the whole course of the molecular dynamics simulation. Otherwise, FORTRAN format runtime errors will occur during writing or reading of the ASCII file. This is of particular concern when one is writing velocities. The default format and scale work well for Cartesian coordinates but do not work for velocities (default=12Z.6, hexadecimal).
OASCii=$<$logical$>$
writes a formatted (ASCII) file if OASCii is TRUE; if OASCii is FALSE, an unformatted (binary) file is written. A scale factor $s$ and an offset $o$ are applied to the coordinates $r$ before they are written to an ASCII file; i.e., $r'=s *r + o$.

OFFSet=$<$real$>$
provides an offset $o$ for the OASCii= TRUE option (default: 800).
ORIEnt { $<$orient-statement$>$ } END
fits the input trajectory frames to the main coordinate set using a least-squares fitting procedure and then writes the frames to the trajectory output file.
OUTPut=$<$filename$>$
designates an output file for the trajectory (default: OUTPUT).
SCALe=$<$real$>$
provides a scale factor $s$ for the OASCii=TRUE option (default: 10000).
$<$orient-statement$>$:==
MASSweighting=$<$logical$>$
is a logical flag indicating whether mass-weighting is applied for the least-squares fitting procedure (default:
FALSE).
NOROtation=$<$logical$>$
is a logical flag indicating whether a rotation is applied to the coordinates. If FALSE, only a translation vector is applied (default: TRUE).
SELEction=$<$selection$>$
specifies the atoms that are used to define the least-squares transformation. However, the transformation is applied to all coordinates (default: (ALL) ).
WEIGhting-with-B=$<$logical$>$
is a logical flag indicating whether the B-array is used for weighting the atoms for the least-squares fitting procedure (default: FALSE).

next up previous contents index
Next: Requirements Up: Merging Trajectories Previous: Merging Trajectories   Contents   Index
Xplor-NIH 2025-03-21