[gmx-users] Is diffusion coefficient dependent on box size?

Smith, Micholas D. smithmd at ornl.gov
Mon Oct 12 16:52:52 CEST 2015

How long are your simulations? Have you looked at your msd.xvg files to make sure you have a "straight" line in the fitting region?


Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Pallavi Banerjee <pallavisept at students.iiserpune.ac.in>
Sent: Monday, October 12, 2015 10:49 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Is diffusion coefficient dependent on box size?

Hello Users,

On simulating SPC-E water, I see that I get two different values of
diffusion coefficient from two different box sizes. I get D=2.4 from a
cubic box of 3 nm and D=2.7 from a cubic box of 7 nm. All the .mdp
parameters are the same for both. The diffusion coefficients are obtained
from g_msd Any idea what could be going wrong here?

Thanks in advance!

-Pallavi Banerjee
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