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)

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

NAME

       g_clustsize - calculate size distributions of atomic clusters

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_clustsize  -f	traj.xtc  -s  topol.tpr  -n  index.ndx	-o  csize.xpm  -ow  csizew.xpm -nc nclust.xvg -mc maxclust.xvg -ac avclust.xvg -hc
       histo-clust.xvg -temp temp.xvg -mcn maxclust.ndx -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -cut real
       -[no]mol -[no]pbc -nskip int -nlevels int -ndf int -rgblo vector -rgbhi vector

DESCRIPTION

       This  program  computes	the  size distributions of molecular/atomic clusters in the gas phase. The output is given in the form of an  .xpm
       file.  The total number of clusters is written to an  .xvg file.

       When the  -mol option is given clusters will be made out of molecules rather than atoms, which allows clustering of  large  molecules.	In
       this case an index file would still contain atom numbers or your calculation will die with a SEGV.

       When  velocities  are  present in your trajectory, the temperature of the largest cluster will be printed in a separate	.xvg file assuming
       that the particles are free to move. If you are using constraints, please correct the temperature. For instance water simulated with  SHAKE
       or  SETTLE  will  yield	a  temperature	that is 1.5 times too low. You can compensate for this with the  -ndf option. Remember to take the
       removal of center of mass motion into account.

       The  -mc option will produce an index file containing the atom numbers of the largest cluster.

FILES

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

       -s topol.tpr Input, Opt.
	Portable xdr run input file

       -n index.ndx Input, Opt.
	Index file

       -o csize.xpm Output
	X PixMap compatible matrix file

       -ow csizew.xpm Output
	X PixMap compatible matrix file

       -nc nclust.xvg Output
	xvgr/xmgr file

       -mc maxclust.xvg Output
	xvgr/xmgr file

       -ac avclust.xvg Output
	xvgr/xmgr file

       -hc histo-clust.xvg Output
	xvgr/xmgr file

       -temp temp.xvg Output, Opt.
	xvgr/xmgr file

       -mcn maxclust.ndx Output, Opt.
	Index 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)

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

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

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

       -cut real 0.35
	Largest distance (nm) to be considered in a cluster

       -[no]molno
	Cluster molecules rather than atoms (needs  .tpr file)

       -[no]pbcyes
	Use periodic boundary conditions

       -nskip int 0
	Number of frames to skip between writing

       -nlevels int 20
	Number of levels of grey in  .xpm output

       -ndf int -1
	Number of degrees of freedom of the entire system for temperature calculation. If not set, the number of atoms times three is used.

       -rgblo vector 1 1 0
	RGB values for the color of the lowest occupied cluster size

       -rgbhi vector 0 0 1
	RGB values for the color of the highest occupied cluster size

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						    g_clustsize(1)