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

[rocwhite168]

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