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trjcat(1) [debian man page]

trjcat(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					 trjcat(1)

NAME

       trjcat - concatenates trajectory files

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       trjcat  -f  traj.xtc  -o trajout.xtc -n index.ndx -demux remd.xvg -[no]h -[no]version -nice int -tu enum -xvg enum -b time -e time -dt time
       -prec int -[no]vel -[no]settime -[no]sort -[no]keeplast -[no]overwrite -[no]cat

DESCRIPTION

	trjcat concatenates several input trajectory files in sorted order.  In case of double time frames the one in the later file is used.	By
       specifying   -settime  you will be asked for the start time of each file. The input files are taken from the command line, such that a com-
       mand like  trjcat -f *.trr -o fixed.trr should do the trick. Using  -cat, you can simply paste several files together  without  removal	of
       frames with identical time stamps.

       One  important  option  is  inferred when the output file is amongst the input files. In that case that particular file will be appended to
       which implies you do not need to store double the amount of data.  Obviously the file to append to has to be the one with  lowest  starting
       time since one can only append at the end of a file.

       If  the	 -demux option is given, the N trajectories that are read, are written in another order as specified in the  .xvg file.  The  .xvg
       file should contain something like:

	0  0  1  2  3  4  5

       2  1  0	2  3  5  4

       Where the first number is the time, and subsequent numbers point to trajectory indices.	The frames corresponding to the numbers present at
       the  first  line  are collected into the output trajectory. If the number of frames in the trajectory does not match that in the  .xvg file
       then the program tries to be smart. Beware.

FILES

       -f traj.xtc Input, Mult.
	Trajectory: xtc trr trj gro g96 pdb cpt

       -o trajout.xtc Output, Mult.
	Trajectory: xtc trr trj gro g96 pdb

       -n index.ndx Input, Opt.
	Index file

       -demux remd.xvg Input, Opt.
	xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 19
	Set the nicelevel

       -tu enum ps
	Time unit:  fs,  ps,  ns,  us,	ms or  s

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -b time -1
	First time to use (ps)

       -e time -1
	Last time to use (ps)

       -dt time 0
	Only write frame when t MOD dt = first time (ps)

       -prec int 3
	Precision for  .xtc and  .gro writing in number of decimal places

       -[no]velyes
	Read and write velocities if possible

       -[no]settimeno
	Change starting time interactively

       -[no]sortyes
	Sort trajectory files (not frames)

       -[no]keeplastno
	Keep overlapping frames at end of trajectory

       -[no]overwriteno
	Overwrite overlapping frames during appending

       -[no]catno
	Do not discard double time frames

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011							 trjcat(1)

Check Out this Related Man Page

g_h2order(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_h2order(1)

NAME

       g_h2order - computes the orientation of water molecules

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_h2order  -f  traj.xtc	-n index.ndx -nm index.ndx -s topol.tpr -o order.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w
       -xvg enum -d string -sl int

DESCRIPTION

	g_h2order computes the orientation of water molecules with respect to the normal of the box. The program determines the average cosine	of
       the  angle between the dipole moment of water and an axis of the box. The box is divided in slices and the average orientation per slice is
       printed.  Each water molecule is assigned to a slice, per time frame, based on the position of the oxygen. When	-nm  is  used,	the  angle
       between the water dipole and the axis from the center of mass to the oxygen is calculated instead of the angle between the dipole and a box
       axis.

FILES

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input
	Index file

       -nm index.ndx Input, Opt.
	Index file

       -s topol.tpr Input
	Run input file: tpr tpb tpa

       -o order.xvg Output
	xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 19
	Set the nicelevel

       -b time 0
	First frame (ps) to read from trajectory

       -e time 0
	Last frame (ps) to read from trajectory

       -dt time 0
	Only use frame when t MOD dt = first time (ps)

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -d string Z
	Take the normal on the membrane in direction X, Y or Z.

       -sl int 0
	Calculate order parameter as function of boxlength, dividing the box in nr slices.

KNOWN PROBLEMS

       - The program assigns whole water molecules to a slice, based on the first atom of three in the index  file  group.  It	assumes  an  order
       O,H,H. Name is not important, but the order is. If this demand is not met, assigning molecules to slices is different.

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						      g_h2order(1)
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