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

[Acoot Brett]

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


----- Original Message -----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
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.

Mark
-- gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists