[gmx-users] Hello

nikhil damle pdnikhil at yahoo.co.in
Tue Jul 14 09:16:14 CEST 2009

So the problem is that .tpr file has peptide shifted in another box as after g_rms with -pbc option, RMSD is still ~1.5A => .tpr file generated from .mdp file during grompp programme, has peptide away from its usual position. I am giving pbc = xyz in .mdp file as well. Why then .tpr file should have peptide displaced ?


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 12:28:05 PM
Subject: Re: [gmx-users] Hello

nikhil damle wrote:
> 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? You need to compare that with pre-simulation...

> So is it a problem at g_rms stage or it is the problem related to PBC and really the peptide is flying off ??

Try trjconv like my link suggested.

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