GROMACS version: 2020.5
GROMACS modification: No
Hi Everyone,
My systems contains a mineral slab with water above it. I am applying position restraints to the mineral slab.
I came across this note: “Removing center of mass motion in the presence of position restraints might cause artifacts. When you are using position restraints to equilibrate a macro-molecule, the artifacts are usually negligible.”
So, would you advise that I set comm-mode to None? Or should I set comm-mode to linear, with comm-grps = everything that’s not being position restrained?
Thank you for your help!
Sincerely,
Tej S. Choksi
Assistant Professor
School of Chemical and Biomedical Engineering
Nanyang Technological University, Singapore
Block N1.2, B1-18, 62 Nanyang Drive
Singapore 637459, Office: +65 6316 8940
Hi,
it depend on the kind of simulation you intend to carry out.
I usually set comm-mode to None every time I have restrained molecules, even for equilibration runs, but this is very specific to my system (I have an interface that need to relax, so there is some non-negligible mass flow that could be hindered if com motion is removed).
I am not sure setting comm-mode to linear, with comm-grps = everything that’s not being position restrained would help; assume that you start with a not-so-equilibrated box where water still doesn’t have the correct density: in this case the com of the water group would possibly get closer or farther from the restrained mineral substrate after equilibration, if comm-mode is set to None. On the other hand, if you remove com motion you may end up either (a) having an incorrect liquid density or (b) having incorrect liquid layering close to the substrare or (c) slowing down thw equilibration run (or maybe (a), (b) and (c), hard to tell). Does it make sense?