MSD-Center of mass

User discussions
1

GROMACS version:
GROMACS modification: No
Hi I need to calculate MSD-center of mass of PSS melt system.
I went through documentation and got below.
I need to know whether this calculates MSD-Center of mas of all the chains.(I have 860 chains-20 monomer system).
gmx msd -f pss_5_400-1000.xtc -s pss5new.gro -n pss5edi.ndx -o msd_pss_5com.xvg -rmcomm yes

Pls advice.

Thanks,
Priya

2

One option is to simply calculate a few frames with another approach you understand and check that you get the same result as your gromacs analysis. (Not to downplay the importance of understanding your gromacs analysis command fully). For example, you could try repeating analysis with mdanalysis or loos or tcl scripting in vmd. Could also use gmx msd -nomw to get a simple center of geometry difference and then gmx traj to output raw coordinates and then compute the center of geometries with awk and do the diff yourself. For the simple answer, if you really want the center of mass difference (e.g., the displacement between two Cartesian points), then no, I don’t think your command will do what you want it to.

3

Thanks