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

[Acoot Brett]

Dear Catch ya,
 
I have watched the trajectory of the simulation. Besdies, I got the PDb file for the whole 10 ns MD every 500 ps. Then I compared all the PDB files generated, and it confirms that 1 specific residues moves in an extremely large space.
 
Can you give me an explaination on it?
 
Cheers,
 
Acoot


----- Original Message -----
From: Dallas Warren <Dallas.Warren at monash.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Wednesday, 8 August 2012 8:58 AM
Subject: RE: [gmx-users] a residue move in extremely large scale in MD

What information has "told you" that you have large scale movement?  Where did that information come from, how was it generated?  Have you watch the trajectory of this simulation to see how the residue actually moves?

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Acoot Brett
> Sent: Wednesday, 8 August 2012 8:30 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] a residue move in extremely large scale in MD
> 
> 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
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