[gmx-users] RE: How to obtain structures with large RMSD?

[Ehud Schreiber]

Hi,

You can try the non-gromacs tool Concoord:
http://www.mpibpc.mpg.de/groups/de_groot/concoord/
http://151.100.52.62/pdf/046_amadei_proteins_1997.pdf

It was used e.g. in the CC/PBSA algorithm
http://ccpbsa.biologie.uni-erlangen.de/ccpbsa/
http://www.nature.com/nmeth/journal/v6/n1/full/nmeth0109-3.html


----------------------------------------------------------------------

Message: 1
Date: Mon, 10 Oct 2011 10:04:30 -0500
From: "Liu, Liang" <liu4gre at gmail.com>
Subject: [gmx-users] How to obtain structures with large RMSD?
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
	
<CABxJRoJ5MgcYx02c5CqjtbU8HhEdh1=CYU1EGgzzqeot0_+76Q at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi, all,

I am trying to use Gromacs to obtain structural ensembles around native
structures (PDB structures).
However the simulated structures are always very close to the initial
one,
with RMSD < 0.2.
I am wondering how to obtain large-RMSD structures? Thanks.

-- 
Best,
Liang Liu