[gmx-users] How to calculate the MSD of center of mass of molecules

Zheng Gong unimisia at gmail.com
Thu Mar 16 06:00:32 CET 2017

Hello everyone,

In my simulation, I want to calculate the MSD of COM of some molecules
using *gmx msd* command.

>From the Gromacs manual, *For molecules consisting of more than one atom,
ri can be taken as the center of mass positions of the molecules. In that
case, you should use an index file with molecule numbers.*

It seems that all i need to do is create an index file with molecule
numbers. Following is my procedure:

*echo 'res_com of resname Tf2N' | gmx select -s nvt-msd.tpr -on mol.ndx*

*gmx msd -f nvt-msd.xtc -s nvt-msd.tpr -n mol.ndx -o msd-com*

However, it does not produce the result what I want. The resulting
msd-com.xvg is not the MSD of COM of Tf2N molecule. It seems that mol.ndx
has not been recognize  as molecule numbers.

Is there anything I missed?

Gong, Zheng
Doctoral Candidate in Physical Chemistry
School of Chemistry and Chemical Engineering
Shanghai Jiao Tong University

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