Periodic-molecules versus pbc=yes for membrane equilibration

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1

GROMACS version: 2020.2
GROMACS modification: Yes/No
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I am equilibrating some planar lipid membrane systems. I wonder what the difference is by applying pbc = xyz versus periodic-molecules=yes. Both seem to bring the system to equilibrium.

Thank you!

2

A membrane is not a periodic molecule; that is intended for use in infinite molecules like CNT, graphene, etc.

3

What would be your advice for setting up a membrane on top of an infinite molecule? So far, only by choosing “periodic-molecules=yes” Gromacs doesn’t complain, but I am not exactly sure what it does to the membrane. I did some tests with membrane-only systems and didn’t observe any significant structural difference

4

The periodic_molecules keyword does nothing if there are no infinite species, but if you include an infinite molecule, it needs to be set to “yes.”

5

Thanks. It’s reassuring.