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

[Acoot Brett]

Dear Justin,
 
Can you explain to me what do you mean for "trjconv -pbc mol -ur compact followed by trjconv -center". Does it mean 2 steps command, with the first step as "trjconv -pbc mol -ur compact" and the second step as "trjconv -center"? Or can we merge it as a single step step?

Second, will you please tell me in " If the outcome of the analysis before and after PBC correction are the same", which analysis can be used as the "outcome" for the analysis?

Thanks.

Acoot
 
----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Acoot Brett <acootbrett at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Saturday, 11 August 2012 10:02 AM
Subject: Re: [gmx-users] a residue move in extremely large scale in MD



On 8/10/12 7:58 PM, Acoot Brett wrote:
> Dear Dr. Dallas Warren,
> 
> My protein is a protein-peptide complex. The residues I mentioned which moves in a large scope is from the peptide, it is the last 3rd residue of the peptide, a lysine.
> I compared this lysine position with the other residue positions (including the peptide binding pocket and the all the peptide residues) with PDB from different time intervals (total MD is 10 ns, and I extracted the PDB every 0.5 ns, and then I align all the PDB files and compared the relative position of this lysine in different PDB files), I find this lysine position changed most significantly during the whole 10 ns MD.
> 

Quantitative analysis is more convincing - RMSD, RMSF, etc.

> In addition, will you please tell me how to analysis whether the phenomenon is from periodid boundary effect? I have no knowledge on how boundary effect affect the MD.
> 

Center the system with iterations of trjconv, i.e. trjconv -pbc mol -ur compact followed by trjconv -center.  If the outcome of the analysis before and after PBC correction are the same, then you can rule out PBC effects, though they should be fairly obvious upon watching the trajectory anyway.

-Justin

-- ========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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