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 and the offset 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 and an offset are applied to the
coordinates before they are written to an ASCII file; i.e.,
.
OFFSet=real
provides an offset 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 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).