[gmx-users] g_msd and MSD analysis

Dommert Florian dommert at icp.uni-stuttgart.de
Sun Jun 10 10:55:53 CEST 2012

On Sat, 2012-06-09 at 15:33 -0700, Mr Bernard Ramos wrote: 
> Hi everyone!
> I have a 20 ns  simulation (2fs timestep but coordinates saved every
> 0.2 ps) and I was able to calculate the mean-square-displacement of
> the oxygen atoms of my water solvent. The entire MSD plot looks very
> linear to me. I need to fit this set of MSD data to obtain the
> diffusion coefficient. However, I am not sure if I will have to use
> the entire MSD points or may be just to consider a few picoseconds at
> the latter part of the simulation time. In papers I have read, they
> use up to a 100 ps, although no mention were made as to where those
> set of points came from.  Please help.


have you looked at a linear graph or on a log-log representation. With
the latter representation, it is much easier to identify the different
regimes of diffusion (ballistic, subdiffusive, and linear). This should
allow you to chose an appropriate fit range. Moreover if you fit a
straight line to the log-log representation you will immediately see,
where the MSD curve deviates from the linear behaviour.


> This post seems to suggest a nanosecond window for the analysis of the
> MSD curve
> http://lists.gromacs.org/pipermail/gmx-users/2012-January/067487.html
> Although, this other one suggests using the latter 40 ps of his MSD
> http://lists.gromacs.org/pipermail/gmx-users/2009-November/046990.html
> Your help is greatly appreciated.
> Thanks,
> Bernard
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Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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