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.
Yes.
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:
http://wiki.gromacs.org/index.php/REMD#Post-processing
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
option.
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...
Thanks!
David
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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.
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