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:
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users