[gmx-users] RMSD

Shima Arasteh shima_arasteh2001 at yahoo.com
Wed Jan 23 18:48:00 CET 2013

I want to find the structure with the lowest RMSD, so I think it does not make different to set any of pdb files as the ref structure.
I made an attempt and got the RMSD regarding the first pdb file. The RMSD relative to -1 for the ref structure, is written in xvg file. Is my approach logically correct?

Thanks for your suggestions.


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, January 23, 2013 7:20 PM
Subject: Re: [gmx-users] RMSD

On 1/23/13 10:38 AM, Shima Arasteh wrote:
> Hi,
> Is it  possible to get RMSD of 10 different pdb files by GROMACS?

Relative to what?  Each other?  Some universal reference?

> g_rms may help?

That, or g_confrms, depending on what you're actually trying to measure.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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