COMM-removal for one group only

User discussions
1

GROMACS version:2023.2
GROMACS modification: No

For post processing purposes, I would like to remove the center of mass motion of one group in my system, without affecting the physics of the simulation. I tried assigning the group as comm-gprs, but gromacs complains about the rest of the molecules not being part of any comm-group. I had assumed that the comm-grps only determine what atoms count for the motion calculation, but that the correction is applied to the whole system. Is this the case, or would this setup introduce fictitious forces acting only on the specified group?

2

For postprocessing purposes you can remove COM motion afterwards. The simulation itself is most important when choosing COM motion removal. COM groups are used both for calculation of the motion and removal. Normally there is no reason to using anything else than a single group containing the whole system.

3

Okay, that makes it clear. Thank you.