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demux - Online in the Cloud

Run demux in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command demux that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



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 trajectories.


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)


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.

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