On 26/07/2012 8:17 PM, ppxasjsm wrote:
Hi Mark,
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
It does the converse of the operation you thought it did.
and why
I need replica_index.xvg and replica_temp.xvg and what trjcat -f *.xtc
-demux replica_index.xvg gives me.
Nobody said you did need them.
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.
http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing says this.
@Mark, if you do have a version, where temperatures are exchanged instead,
would it be somehow possible to obtain this?
No, I don't have the time right now to make even an alpha-quality
version available and roughly documented. It'd only be useful if you
were running on hundreds of processors for hundreds of nanoseconds, and
likely only under noisy network conditions, anyway.
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
different energy?
If nstenergy is a suitable value wrt mdrun -replex, it will be the
potential energy in the .edr file, which you can approximately verify
from the .log file.
Mark
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