Dear Daniel,
thanks a lot! I will try it :)
All the best,
Nick
Message: 17
Date: Fri, 9 Feb 2018 08:40:49 -0500
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] Certain statistics from the trajectory
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAAC0qOa+Q1CBScVUiHT9SrVLwOhvTitSzozgNB1PJ_8WsP8oYg.mail.gmail.com>
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Hi,
You can do this with cpptraj once you have your forces. If you didn't
write forces during the simulation you can obtain them via
post-processing with sander (imin=5) and setting ntwf to 1 - see the
manual for full details.
Once you have the force trajectory you can read it in with cpptraj and
use the 'average' action to calculate the average over all frames. If
you read in a combined coordinates/force NetCDF trajectory make sure
you use the 'usefrcascoords' keyword to use forces in place of the
coordinates.
Hope this helps,
-Dan
On Wed, Feb 7, 2018 at 6:54 AM, Nikolay N. Kuzmich <nnkuzmich.gmail.com>
wrote:
> Dear AMBER users and developers,
>
> I would like to ask you if it is possible to obtain the following
statistics
> from the MD trajectory in AMBER - the question is how to compute the mean
> force acting on each atom of a (partially restrained) macromolecule.
>
> Kind regards,
> Nick
>
> Nikolay Kuzmich
> Department of Drug Safety,
> Research Institute of Influenza,
> WHO National Centre of Russia,
> 15/17 Professor Popov St.,
> Saint-Petersburg
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Feb 12 2018 - 01:30:01 PST
