[gmx-users] replica exchange output information
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jan 8 09:29:14 CET 2008
David Mobley wrote:
> I have further replica exchange questions...
>>>> The order is that from low temperature to high temperature (as you could
>>>> check from the edr files) and when swaps happen the coordinates and
>>>> boxes are exchanged between CPUs.
>>> OK. In other words the replicas are always ordered by temperature.
> OK, so can you explain the output of demux.pl, then? In particular,
> I'm wondering what the values in replica_temp.xvg tell me. If the
> replicas are always ordered by temperature, then what do the numbers
> in there refer to? i.e., if index #0 always describes the simulation
> at the lowest temperature, then what does the number in the second
> column of replica_temp.xvg represent?
> It would be nice to have this sort of information (i.e. that demux.pl
> exists, and what it does) in the documentation or on the REMD page of
> the wiki.
I've tried to write a bit about it:
>> More info is usually better, however demux.pl md0.log should get you
>> going. Meanwhile, as you probably are aware, we are considering some
>> other REMD varieties, and that will probably mean we will need to add
>> more info.
> I've done that, but the output is not described except by its names
> ('replica_temp.xvg', 'replica_index.xvg') and telling me that I can
> run these through trjcat to demultiplex. It is unclear from the
> documentation of both programs what I would achieve if I used this
> Maybe adding information as features are added would be the way to go?
> Then the documentation wouldn't lag behind the features.
In an ideal world, yes...
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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