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

[Matthew Zwier]

Hi Ruhollah,

A while ago on the list there was a discussion of extreme memory use
and possibly-incorrect results from g_msd under some conditions.  The
problem could be worked around by imaging the trajectory with trjconv
first to remove jumps across the box, then running g_msd on the
results.  Perhaps you'll have some more success with that workflow.

Cheers,
Matt Z.

On Fri, Dec 9, 2011 at 6:30 PM, Ruhollah Moussavi-Baygi
<ruhollah.mb at gmail.com> wrote:
> 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 [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...
>> [2]
>>
>>
>> Mark
>
> Read more
> http://support.scalalife.eu/content/diffusion-coefficient#comment-103
>
>
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>
> [1] http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant
> [2]
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
>
>
>
> --
> Best,
> Ruhollah Moussavi-Baygi
>
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