[gmx-users] Gromacs MSD close to an slab/interface

Tuanan Lourenço lourenco.tuanan at gmail.com
Tue Sep 18 21:26:00 CEST 2018

Hi everyone,

I have a simulation with a metal slab and I would like to get the MSD of
the molecules close to the slab. I have tried the gmx selection that works
pretty well to structural analysis, but to the dynamical analysis such as
msd or rotacf there are some issues. I have tried the dynan_mol_com flag in
the gmx selection. But it is writing a huge index file, in which each group
index is the number of the molecules close to the slab in a specific frame.
I would like to know if it is possible to put a restriction in the gmx msd
and get the MSD in a specific box region.


MSc. Tuanan C Lourenço
Ph.D Student Physical Chemistry - Universidade Federal Fluminense
Molecular Modelling and Computer Simullation Group - UFF
MOLMOD-CS WEBSITE <http://www.molmodcs.uff.br/>

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