[gmx-users] Re: Problem with REMD
ppxasjsm at nottingham.ac.uk
Thu Jul 26 12:17:53 CEST 2012
>You're not the first to make this wrong assumption, but GROMACS actually
>exchanges coordinates among (sets of) cpus, which write to the same
>output file, i.e. the trajectories written by mdrun are already at
>constant temperature. (That's inefficient because you have to re-do the
>domain decomposition, and is likely an artefact of the pre-existing
>mdrun -multi functionality from which the REMD implementation derives. I
>have a private GROMACS version off 4.5.5 that scales better to large
>processor sets by exchanging only T (and some minor details) and only
>doing pairwise communication during exchange attempts - however if it
>sees the light of day, it would be in at least GROMACS 5.0.)
Ok if i understand this correctly, my output files md0.xtc, md1.xtc ...
correspond to the original temperatures set in md0.mdp, md1.mdp etc..., so I
can just straight away build my Ramachandran diagran from these.
Then I don't quite understand what the script demux.pl actually does and why
I need replica_index.xvg and replica_temp.xvg and what trjcat -f *.xtc
-demux replica_index.xvg gives me.
It seems very counterintuitive to change configurations rather than
temperatures, it would be nice if this was explicitly stated in the REMD
gromacs reference page.
@Mark, if you do have a version, where temperatures are exchanged instead,
would it be somehow possible to obtain this?
Thanks for resolving this.
One last question regarding this. The energy, which is used for calculating
the exchange probabilities, does this correspond to the potential energy,
which can be extracted from g_energy -f file.edr < 11 0, or is it a
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