[gmx-users] Hello

nikhil damle pdnikhil at yahoo.co.in
Tue Jul 14 08:49:52 CEST 2009

I am turning pbc =xyz as written in earlier correspondence. But in spite of this when i run g_rms after simulation, my initial structure itself shows ~1.5 nm rmsd. So is it a problem at g_rms stage or it is the problem related to PBC and really the peptide is flying off ??


From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, 14 July, 2009 12:07:24 PM
Subject: Re: [gmx-users] Hello

nikhil damle wrote:
> I am carrying out energy minimization of the protein peptide complex. But even after using nstcomm=1 and/or pbc=xyz, my energy minimized structure has peptide far away from the binding site. This did not happen with ATP-protein complex. Even in Drug-enzyme tutorial, similar .mdp file is given for energy minimization. What could be possible reasons for such flying away of the peptide ? How should I fix the problem ?

Please use a descriptive subject line, not a generic greeting.

You are probably seeing a periodicity artefact. See http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions

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