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

NAME

       g_rmsf - calculates atomic fluctuations

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_rmsf  -f  traj.xtc  -s  topol.tpr  -n	index.ndx  -q  eiwit.pdb -oq bfac.pdb -ox xaver.pdb -o rmsf.xvg -od rmsdev.xvg -oc correl.xvg -dir
       rmsf.log -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -[no]res -[no]aniso -[no]fit

DESCRIPTION

	g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions in the trajectory (supplied with  -f)
       after (optionally) fitting to a reference frame (supplied with  -s).

       With option  -oq the RMSF values are converted to B-factor values, which are written to a  .pdb file with the coordinates, of the structure
       file, or of a  .pdb file when  -q is specified.	Option	-ox writes the B-factors to a file with the average coordinates.

       With the option	-od the root mean square deviation with respect to the reference structure is calculated.

       With the option	-aniso,  g_rmsf will compute anisotropic temperature factors and then it will also output average coordinates and a   .pdb
       file with ANISOU records (corresonding to the  -oq or  -ox option). Please note that the U values are orientation-dependent, so before com-
       parison with experimental data you should verify that you fit to the experimental coordinates.

       When a  .pdb input file is passed to the program and the  -aniso flag is set a correlation plot of the Uij will be created, if  any  aniso-
       tropic temperature factors are present in the  .pdb file.

       With  option   -dir  the average MSF (3x3) matrix is diagonalized.  This shows the directions in which the atoms fluctuate the most and the
       least.

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

       -q eiwit.pdb Input, Opt.
	Protein data bank file

       -oq bfac.pdb Output, Opt.
	Protein data bank file

       -ox xaver.pdb Output, Opt.
	Protein data bank file

       -o rmsf.xvg Output
	xvgr/xmgr file

       -od rmsdev.xvg Output, Opt.
	xvgr/xmgr file

       -oc correl.xvg Output, Opt.
	xvgr/xmgr file

       -dir rmsf.log Output, Opt.
	Log 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

       -[no]resno
	Calculate averages for each residue

       -[no]anisono
	Compute anisotropic termperature factors

       -[no]fityes
	Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure  and  the	trajectory
       match.

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011							 g_rmsf(1)