[gmx-users] replica exchange output information

[Berk Hess]

>From: "David Mobley" <dmobley at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] replica exchange output information
>Date: Mon, 7 Jan 2008 10:40:44 -0800
>
>David,
>
> > 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.
>
> > >
> > > As a follow-up question, is there an easy way (i.e. some output file
> > > written) to track which replica number is at a particular temperature
> > > (equivalently, a log of swaps between replicas)? I'd like to be able
> > > to monitor mixing between my replicas.
> >
> > Yes, check src/contrib/scripts/demux.pl
>
>OK. It would still be nice to have documented what goes into the log
>file in sufficient detail that I could use the info myself (i.e. to
>write a python code that would do something similar).

grep Repl md0.log gives:

Initializing Replica Exchange
Repl  There are 6 replicas:
Repl      0     1     2     3     4     5
Repl  T 300.0 350.0 410.0 480.0 560.0 650.0
Repl
Repl  exchange interval: 1000
Repl  random seed: 525106
Repl  below: x=exchange, pr=probability
Replica exchange at step 1000 time 2
Repl 0 <-> 1  dE =  2.492e+00
Repl ex  0    1    2    3    4    5
Repl pr   .08       .00       .13
Replica exchange at step 2000 time 4
Repl ex  0    1    2    3 x  4    5
Repl pr        .00       1.0
...

Which is a very short explanation, but should hopefully provide
enough information.

Berk.

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