[gmx-users] replica exchange output information
dmobley at gmail.com
Mon Jan 7 23:11:18 CET 2008
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
> 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.
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