[gmx-users] Unexpected behavior of g_msd

Berk Hess gmx3 at hotmail.com
Fri Nov 27 13:23:14 CET 2009

> To: gmx-users at gromacs.org
> Date: Thu, 26 Nov 2009 19:43:00 +0000
> From: darrellk at ece.ubc.ca
> Subject: [gmx-users] Unexpected behavior of g_msd
> Hi Berk,
> I am thinking that you mean that MSD is a function of the time
> differences and the number of time differences. In other words, if the
> simulation is too short, then GROMACS would not have enough time
> differences to accurately calculate a diffusion constant since the slope
> of the msd versus time within these time intervals would vary too much.
> Thus, I thought that, in order to get an accurate measurement of
> diffusion, it was necessary to run the simulation for a long enough
> period of time to get into a region where there is a linear relationship
> between msd & time so that the regression fit is improved. Is this
> correct?

That's correct.

> In the paper "The Working Man’s Guide to Obtaining Self Diffusion
> Coefficients from Molecular Dynamics Simulations", they indicate that a
> simulation time of approximately 2 ns is appropriate for gas phase
> simulations and that the section of time interval used for calculating
> the diffusion constant be the linear region near towards the end of the
> simulation.

This will depend VERY much on the type of system and the state point.


> Thanks.
> Darrell
> >Date: Thu, 26 Nov 2009 11:34:02 +0100
> >From: Berk Hess <gmx3 at hotmail.com>
> >Subject: RE: [gmx-users] Unexpected behavior of g_msd
> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >Message-ID: <COL113-W20188A074F24AF04DD1C638E9B0 at phx.gbl>
> >Content-Type: text/plain; charset="iso-8859-1"
> >
> >
> >NO!
> >The MSD is NOT a function of the trajectory time!
> >The MSD is a function of time differences.
> >For example:
> >if trestart=10 and -b=60 then MSD(4) in the output is the average of the the MSD
> >between 64 and 68, 74 and 78, 84 and 88, etc.
> >
> >Berk
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