N-J.M. Macaluso wrote:
Hello,
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.
Mark
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