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 ??
Regards,
Nikhil
________________________________
From: Mark Abraham <mark.abra...@anu.edu.au>
To: Discussion list for GROMACS users <gmx-users@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
Mark
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