[gmx-users] how to use demux.pl for REMD analysis
Mark.Abraham at anu.edu.au
Thu May 10 00:35:11 CEST 2007
N-J.M. Macaluso wrote:
> I've been reading all of the archived questions on the analysis of
> REMD in Gromacs, and I'm still a bit confused. It appears that the first
> step is to use the demux.pl script to demultiplex the REMD trajectories.
> How to use this script, and what exactly this is supposed to accomplish?
> After this is finished, how do I trace the temperature evolution of a
> single replica?
mdrun returns (discontinuous) trajectories for each temperature. Only if
you don't want these is demux.pl "the first step". Somehow (read the
archives or the script itself for details, I expect) you need to
construct a .xvg file that describes the exchanges, and you can demux
these trajectories to get non-physical but continuous trajectories of
individual structures, if you want them.
More information about the gromacs.org_gmx-users