Re: [AMBER] Checking multiple production run

From: Gustavo Seabra <>
Date: Sat, 3 Jul 2010 10:18:11 -0300

On Saturday, July 3, 2010, nicholus bhattacharjee
<> wrote:
> Dear community,
> I am running multiple production run of same system. Now to check that they
> are giving the similar trajectories which properties should be monitored? I
> am checking RMSD and Rg values. Can anybody suggest any other possible
> properties which I can incorporate? Thank you in advance.

Is there a reason you would expect the trajectories to be similar?
even with exactly the same input files, one would expect trajectories
in two distinct runs in the same machine to start diverging after
about 500 steps or so. An usually more significative question is
whether the runs are sampling different regions of the phase space
equally, and you can check that only by comparing average properties
of your system.

now, if for some reason you are really interested in the similarity
among the trajectories, I'd recommend that you take a look at the work
by Dan Sindhikara, J. Chem. Theory Comput., 2009, 5 (6), pp 1624–1631.
I believe he describe some metrics to compare two trajectories there.


Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
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Received on Sat Jul 03 2010 - 06:30:03 PDT
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