Re: [AMBER] "Free energy fluctiontions over trajectory in"

From: Vlad Cojocaru <>
Date: Wed, 13 May 2015 16:04:36 +0200

You can dump the output into a file using the "-eo" option (see part of the AMBER manual).


On 05/13/2015 03:55 PM, James Starlight wrote:
> Dear Amber users!
> Based on the mmgbsa outputs (including both dG and decomposition
> outputs) I'd like to monitor fluctuations of the total dG over the
> trajectory (and possible to see both dH and dS dynamics). Also I'd
> like to do the same on the per-residue basis (E.g to see how dH
> fluctuate for several chosen residues). I'd be thankful if someone
> provide me what flags should I activate in the mmgbsa input file and
> what output files will contain that information?
> Thanks!
> James
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Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
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Received on Wed May 13 2015 - 07:30:02 PDT
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