[gmx-users] How to compute self diffusivities when the xtc trajectory file contains only a subset of atoms

Mark Abraham mark.j.abraham at gmail.com
Sun Sep 28 08:32:09 CEST 2014


I'm not sure this will help, because I'm not sure what the origin of the
problem is, but you can easily hack a copy of your .top so that a fresh run
of grompp will produce a .tpr that will match the .xtc.

On Sep 28, 2014 7:47 AM, "rocwhite168" <rocwhite168 at 163.com> wrote:

> Dear GROMACS users,
> I'm trying to compute mean square displacements for molecules. My
> system contains atoms that don't move, so I used "compressed-x-grps"
> in grompp.mdp to exclude them from the xtc trajectory file. After
> mdrun, I ran "gmx convert-tpr -s topol.tpr -n index.ndx" to reduce the
> set of atoms in the tpr file to match those in the xtc file (otherwise
> "gmx msd" will fail because the atom indices exceed those found in the
> xtc file). Say, for both "compressed-x-grps" and "gmx convert-tpr" I
> specified OW_HW to include all water molecules. However, tpxout.tpr
> generated by "gmx convert-tpr" treats all water molecules as a large,
> single molecule, and as a result "gmx msd" detects only that one
> molecule. This would be useful for computing corrected diffusivities,
> but is there a way to let "gmx msd" detect individual molecules
> correctly if I want to compute self diffusivities?
> Any suggestions would be very much appreciated!
> Thanks,
> Roc
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