MSD for center of mass

User discussions
1

GROMACS version:
GROMACS modification: No
Hi all,

I am new to GROMACS. I am currently doing analysis for my system and trying to run MSD analysis. I want to do MSD for COM of my molecules (150 molecules in my system with varying number of atoms in each molecule). It states I need to run
gmx msd [ -o [<.xvg>] ] [ -mol [<.xvg>] ] [ -pdb [<.pdb>] ] [ -b ]

I am a little confused about how to run this and how to get the file (i think it’s diff_mol.xvg) which has the index for start and end atoms for each molecule (or how it should be).
I haven’t specified the molecules at the beginning (Should it come when building the system? if so how do you do it?).

Thank you
Best
ckosgal

2

Hi,
the option -o -mol -pdb -b are just output options, to run you need to provide input files.
To provide input file you can use -f for trajectory file from your simulation
-s tpr file for structure and mass information
-n index file where you define specific group for the analysis.
Best regards
Alessandra