[gmx-users] How to calculate the MSD of center of mass of molecules
unimisia at gmail.com
Thu Mar 16 06:00:32 CET 2017
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?
Doctoral Candidate in Physical Chemistry
School of Chemistry and Chemical Engineering
Shanghai Jiao Tong University
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