[gmx-users] Fwd: PBC issues with membrane-peptide simulation

[Abhi Acharya]

Dear Gromacs users,

I am trying to simulate a system consisting of a lipid bilayer and few
peptides. The peptides have been added randomly to the simulation box only
on one side of the membrane. I ran a 100 ns simulation of the system using
CHARMM36 forcefeild. However, I find that within the first few ns, some of
the peptides appear on the other side of the membrane. I think that this is
because of the diffusion of the peptides though the periodic boundary.
Kindly suggest  how to tackle this problem. I have used COM motion removal
on the whole system for the said simulation.

Regards,
Abhishek Acharya