xplor2gmx(1) General Commands Manual xplor2gmx(1)NAME
xplor2gmx - Convert XPLOR distance restraints to Gromacs format
SYNOPSIS
xplor2gmx (residue offset) input.pdb
DESCRIPTION
xplor2gmx reads an XPLOR input file with distance restraint data as sometimes is found in the pdb database (http://www.pdb.org). From this
input file dihedral restrints should be removed, such that only distance restraints are left. The script can handle ambiguous restraints.
It converts the distance restraints to GROMACS format.
A restraints file (.dat) should be provided on STDIN, and a suitable output file (.itp) is sent to STDOUT.
EXAMPLES
xplor2gmx.pl 33 conf.pdb < restraints.dat > disre.itp
OPTIONS
xplor2gmx requires two command line options: first, the residue offset (integer); second, the .pdb filename. The pdb file must have cor-
rect atom numbers.
SEE ALSO gromacs(7)GROMACS suite, Version 4.0 13 Oct 2008 xplor2gmx(1)
Check Out this Related 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)
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