[gmx-users] Strange behaviour of bonds

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Jun 17 17:50:49 CEST 2012

OK, thanks.
But may these lines in md.mdp file change the result and solve the problem?
; COM motion removal
; These options remove motion of the protein relative to the solvent/ions
nstcomm         = 1
comm-mode       = Linear
comm-grps       = Protein_Water 

 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, June 17, 2012 7:00 PM
Subject: Re: [gmx-users] Strange behaviour of bonds

On 6/17/12 10:23 AM, Shima Arasteh wrote:
> Hi all,
> I simulated a protein in water. When I get its 20 ns trajectory and load it in
> VMD, I see some bonds stretch suddenly and moves far strangely! Is this problem
> because of the wrong structure of the protein? Or I may put some restrains on
> system and solve this problem?
> Anybody may suggest me in this about?

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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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