demux(1) [debian man page]

demux(1)						      General Commands Manual							  demux(1)

NAME

       demux - Convert XPLOR distance restraints to Gromacs format

SYNOPSIS

       demux md0.log extra

DESCRIPTION

       If  you	would  like to make your trajectories continuous again you can use demux to read your md0.log file (you can concatenate several if
       necessary) and produce a few output files. One of these is a .xvg file (replica_ndx.xvg) that can be passed to  trjcat(1)  along  with  the
       original  trajectory  files,  in  order to produce continuous trajectories. The other file (replica_temp.xvg) contains the temperatures for
       each replica, starting at the original temperature. So if your replica of interest starts at, say, 300 K, you  can  follow  its	trajectory
       through	temperature  space.  It  would	be  interesting to add some functionality to make histograms of temperature distributions for each
       replica, which according to most authors, should be flat. The demuxed trajectories can be used with g_kinetics(1) to obtain protein folding
       kinetics from REMD trajectories.

OPTIONS

       md0.log Log file of the trajectory run you wish to make continuous.  Multiple files can be appended together.

       extra Number of times each entry in the log file will be copied.  (Integer)

LIMITATIONS

       If  your  exchange was every N ps and you saved every M ps you can make for the missing frames by setting extra to (N/M - 1). If N/M is not
       integer, you're out of luck and you will not be able to demux your trajectories at all.

SEE ALSO

       gromacs(7), trjcat(1), g_kinetics(1), <http://wiki.gromacs.org/index.php/REMD>

GROMACS suite, Version 4.0					    13 Oct 2008 							  demux(1)

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

NAME

       trjorder - orders molecules according to their distance to a group

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       trjorder  -f  traj.xtc  -s  topol.tpr -n index.ndx -o ordered.xtc -nshell nshell.xvg -[no]h -[no]version -nice int -b time -e time -dt time
       -xvg enum -na int -da int -[no]com -r real -[no]z

DESCRIPTION

	trjorder orders molecules according to the smallest distance to atoms in a reference group or on z-coordinate  (with  option   -z).   With
       distance ordering, it will ask for a group of reference atoms and a group of molecules. For each frame of the trajectory the selected mole-
       cules will be reordered according to the shortest distance between atom number  -da in the molecule and all  the  atoms	in  the  reference
       group.  The  center of mass of the molecules can be used instead of a reference atom by setting	-da to 0.  All atoms in the trajectory are
       written to the output trajectory.

	trjorder can be useful for e.g. analyzing the n waters closest to a protein.  In that case the reference group would be  the  protein  and
       the  group of molecules would consist of all the water atoms. When an index group of the first n waters is made, the ordered trajectory can
       be used with any Gromacs program to analyze the n closest waters.

       If the output file is a	.pdb file, the distance to the reference target will be stored in the B-factor field in order to color	with  e.g.
       Rasmol.

       With option  -nshell the number of molecules within a shell of radius  -r around the reference group are printed.

FILES

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

       -s topol.tpr Input
	Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
	Index file

       -o ordered.xtc Output, Opt.
	Trajectory: xtc trr trj gro g96 pdb

       -nshell nshell.xvg Output, 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

       -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)

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

       -na int 3
	Number of atoms in a molecule

       -da int 1
	Atom used for the distance calculation, 0 is COM

       -[no]comno
	Use the distance to the center of mass of the reference group

       -r real 0
	Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein

       -[no]zno
	Order molecules on z-coordinate

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						       trjorder(1)