[gmx-users] a residue move in extremely large scale in MD

Acoot Brett acootbrett at yahoo.com
Wed Aug 8 00:30:01 CEST 2012

Dear Marck,
Will you please give me some suggestions on how to decide whether the probelm is from periodic boundary conditions?

----- Original Message -----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, 6 August 2012 10:31 PM
Subject: Re: [gmx-users] a residue move in extremely large scale in MD

On 6/08/2012 8:58 PM, Acoot Brett wrote:
>   Dear All,
> I have a protein with about 400 amino acids. I have done a production MD of it. I find in the 400 amino acids, there is 1 amino acids, during the whole MD process, this residue moves in a extremely large scope in comparison with all the other residues.
> Do you think this single residue with extremely large-scale movement in the whole MD has important biological function, or has no biological function?

I'd start by proving that it was not a problem with periodic boundary conditions! If real, movement may or may not be indicative of functional significance - the question is impossible to answer out of context.

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