demux - Convert XPLOR distance restraints to Gromacs format
demux md0.log extra
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
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.
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.
gromacs(7), trjcat(1), g_kinetics(1),