COM pulling of large groups:

User discussions
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1

GROMACS version: 2020.2
GROMACS modification: Yes

Hi, I am trying to keep 13 separate 1nm sized dye molecules aggregated by pulling each molecule towards the center of mass of all groups. By indexing all atoms of all 13 groups as a 14th group called 13Dyes, I tell gromacs in the mdp file to individually pull each dye molecule towards group 14.

However, no matter how large my box size is, I keep getting the following error at one point in my simulations:

“When the maximum distance from a pull group reference atom to other atoms
in the group is larger than 0.5 times half the box size a centrally
placed atom should be chosen as pbcatom. Pull group 1 is larger than that
and does not have a specific atom selected as reference atom.”

Now I made sure to increase my box size enough so that it will be bigger than the dimensions of the aggregate. The aggregate size is up to 2nm, the box size is at least 7nm.

I believe that the problem is that at some point in the simulation, one of dye atoms reaches the simulation box edges, and it fails to work with PBC conditions. I assume that this is the reason in the error it requires a pbc_atom selection. What do you guys think?

Also, if I listen to it, and select a specific pbc_atom, will it constantly be pulling towards this atom? If it will only use it when it reaches the box edges, then it is likely that this atom will no longer be near the actual center of mass of group 14 after some time, and pulling towards an atom located somewhere not near the center of mass will disrupt the structure of the dyes which I am aiming to analyze.

Thanks to anyone willing to help.
Best regards,
Ilan

2

By specifying an atom as reference atom for calculating the COM for a group, it does not mean that you will be pulling towards only that atom. The meaning is that that atom will be used for periodic box treatment, i.e. to make sure that crossing the periodic boundary works as expected when calculating the center of mass. If you don’t specify what atom you should use as reference, the COM might be completely wrong, as the wrong periodic image of some atoms may be used.

I would recommend using the pbcatom option as well as the pull-pbc-ref-prev-step-com option. That way you should avoid any problems crossing the periodic boundary.