How to remove the PBC effect in the .trr file?

User discussions
1

GROMACS version:2020.2
GROMACS modification: No
Dear all gmx-users,
I want to calculate the center of mass (COM) for my molecules under PBC for further research. Due to the PBC, the molecule is broken up at the boundary. I think gmx trjconv command with -pbc mol may works, but how does it deal with the different parts in different box images of the same molecule in boundary? Could someone give me some advice?

Thank you in advance!~

LM

2

Fastest way is to try it and see. Only takes a little while to see what it can do, and if it fixes the issue you have. Much faster than waiting for a response from someone on the discussion board here.

You probably should make the molecules whole first. -pbc mol doesn’t always work how you expect, i.e. 8 molecules at the corners of the simulation box has their COM at the center of the box. You may have to select a single molecule or residue to get it to behave as you expect.