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

[Rausch, Felix]

That's hard to judge for everyone but you, because there are too many questions left. What kind of residue is it? Is it at one of the protein termini, is it on the surface or buried by other sections? Are there interactions with other parts of the system? Did you check the RMSD or RMSF-values for this residue and the protein in general? What exactly does "extremely large" mean? ...
Of course, if the re-centering of the trajectories worked well then these observations should have a reason. Maybe it would be helpful to start the simulation again with a slightly different starting conformation to exclude a simulation artifact of some kind.

Cheers,
Felix

-----Ursprüngliche Nachricht-----
Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Im Auftrag von Acoot Brett
Gesendet: Mittwoch, 8. August 2012 09:00
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] a residue move in extremely large scale in MD

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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