Re: [AMBER] Checking multiple production run

From: Jason Swails <>
Date: Sat, 3 Jul 2010 07:22:04 -0400

Some care should be taken in using the RMSD as a metric for measuring
similarity. If the RMSD values are similar, all that really tells you is
that the trajectories are migrating about the same distance from the
starting frame. However, there is an incredibly large number of ways that
an RMSD can reach, for instance, 5 , so just because 2 RMSDs are 5 from
the same structure tells you nothing about how similar they are to each
other. You may consider comparing the average structures (perhaps looking
at the RMSD of all of the average structures to see how large those are).
You can also plot some ramachandran plots of key residues to see that the
secondary structure is the same. Another option is to use clustering
algorithms and see if you get more or less the same clusters (and members of
those clusters) for each simulation.

Hope this helps,

On Sat, Jul 3, 2010 at 4:41 AM, 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.
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sat Jul 03 2010 - 04:30:03 PDT
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