Gromacs MSD

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

Hi,I want to calculate MSD - center of mass (COM) of a polymer system using gromacs.
Can I know how to do that?

Regards,
Priya

2

GMX traj, option -com gmx traj — GROMACS 2020-beta2 documentation
For example for center of mass for my ring in polar head in my lipid for z coordinates I used for one frame
gmx traj -f eq1_merged_dt_100.xtc -s eq3.tpr -n dgdg_rings.ndx -com -nox -noy -ox dgdg_com_bottom_$number.xvg -b 100000 -e 100000

3

Thanks,
Do you know how to create ndx files?

4

Yeah sure. You need use gmx make_ndx gmx make_ndx — GROMACS 2022.2 documentation

5

Thank you