[gmx-users] Using "gmx msd"

Wes Barnett w.barnett at columbia.edu
Sat Sep 2 13:11:35 CEST 2017

> I went through your tutorial and it is very helpful for beginners like me.
> You have discussed "one methane in water" to calculate RDF...
> Can we follow the same procedure  to compute the diffusion co-efficient of
> methane at the end of the production MD, using gmx msd instead of gmx rdf?
> Or should we change the parameters to calculate MSD?

Hi Vidya,

I have cc'd the GROMACS mailing list.

After the simulation you need to postprocess your xtc file so that it is
"unwrapped"; otherwise, your msd will be artificially low, since the
methane molecule will have gone across the peridiodic boundary condition
several times.

I believe you need to use "gmx trjconv" with the "-pbc nojump" option. Then
you can run "gmx msd" on the new xtc file. See "man gmx-trjconv" for more
information on how to use the "nojump" option.

James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu

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