On 12/10/11 3:23 AM, Matthew Zwier wrote:
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.
All of this is not necessary.
You should first try to do more tests before you claim a bug. For
instance, compute the msd of a single Ca atom.
Furthermore you do not state how your simulation was done and how long
it was. Since you have a single molecule statistics will be poor unless
you simulate for 100 ns or so.
Cheers,
Matt Z.
On Fri, Dec 9, 2011 at 6:30 PM, Ruhollah Moussavi-Baygi
<[email protected]> 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<[email protected]>
Date: Fri, Dec 9, 2011 at 12:17 AM
Subject: Comment for Forum topic: diffusion coefficient
To: [email protected]
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
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Best,
Ruhollah Moussavi-Baygi
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David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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