[gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC

[Ruhollah Moussavi-Baygi]

David,
thank you for your reply.

but, g_msd gives a diffusion coefficient which is one order of magnitude
higher than expected for a small polypeptide (15 res long with gyration Rg
~ 0.8nm) with the same size. this is command line i used:
g_msd-mpi -f  md_mine_2nd.xtc -s  md_mine_2nd.tpr -o  msd_2nd.xvg

when visualizing, I can see that the polypeptide crosses the boundary
several times. apparently,  g_msd counts these 'artificial' jumps in MSD
calculation.  and, that's probably why the diffusion coefficient is
calculated such high (i.e. 500 um2/s for a small protein).

if this is the case, it is a bug in g_msd I believe.

is there any way to get round this problem?

---------- Forwarded message ----------
From: Anonymous <rossen at kth.se>
Date: Fri, Dec 9, 2011 at 12:17 AM
Subject: Comment for Forum topic: diffusion coefficient
To: ruhollah.mb at gmail.com


Hi ruhollahmoussavi-baygi,

Comment by davidvanderspoel: diffusion coefficient


On 2011-12-09 08:34, Mark Abraham wrote:
> On 9/12/2011 5:53 PM, Ruhollah Moussavi-Baygi wrote:
>> I want to calculate the diffusion coefficient of a small polypeptide
>> with g_msd (see here
>> http://www.gromacs.org/**Documentation/How-tos/**Diffusion_Constant<http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant>[1])
>>
>> because of periodic boundary condition, when the peptide goes out of
>> the right side it comes in from left side, which leads to an
>> artificial displacement. this will give rise to a non-realistic MSD.
>>
>> is g_msd intelligent enough to avoid this artificial displacement?
>>
>
Yes it is.


> Not sure about g_msd, but you can take care of it yourself with a
> workflow derived from the information here
> http://www.gromacs.org/**Documentation/Terminology/**
Periodic_Boundary_Condi.<http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condi.>..
[2]
>
>
> Mark

Read more http://support.scalalife.eu/**content/diffusion-coefficient#**
comment-103<http://support.scalalife.eu/content/diffusion-coefficient#comment-103>


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[1] http://www.gromacs.org/**Documentation/How-tos/**Diffusion_Constant<http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant>
[2] http://www.gromacs.org/**Documentation/Terminology/**
Periodic_Boundary_Conditions<http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions>




-- 
Best,
Ruhollah Moussavi-Baygi
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