COM motion removal group

User discussions
1

GROMACS version: 2021.4
GROMACS modification: No

Dear gmx users,

Q1

Referring to the answer of justin tutorial or gmx forum,

When protein in water simulation,
comm-grps = system
tc-grps = protein non-protein

The manual says to make tc-grps and comm-grps the same.
comm-grps = protein non-protein
tc-grps = protein non-protein

So, I’m confused which group I should to use.

Q2

In protein in water simulation,
When there are a number of free ligands to simulate their binding process to the active site,
Does these free ligands belong to “protein” or “non-protein” for tc-grps?

Also, does comm-grps set to system?

Kind Regards,

2

Can you point to where the manual says this? I do not see any such statement, nor do I ever recall this.

Setting tc-grps = protein non-protein in a simple aqueous system can lead to instability if the COM motion corrections collide with one another. I’ve seen that happen, and such a setting is inappropriate.

By default, they will be in the Non-Protein group. There is no straightforward answer for how to apply temperature coupling in this case, as the ligands may come and go from binding sites, but I doubt there is any substantial error by coupling them with the rest of the Non-Protein group.