Maintaining PBC on Collective Variables

From: Malay Ranjan Biswal (
Date: Mon Jul 10 2017 - 08:17:30 CDT

Dear all namd users,

We are doing a lipid bilayer simulation, where we use metadynamics to study insertion of molecules into the membrane. During the simulation, we observe that the membrane translates leaving an apparently split membrane in the minimum image, i.e, lower half of membrane on the top of the box, upper half at the bottom, and water in the middle of the frame. We are using the colvar module to define the z-distance (“distanceZ”) and radius of gyration (“gyration”) as the collective variables for the calculation. However, the PBC is not maintained for these CVs. But by default the “forceNoPBC = off” is active as seen in the log-file. Both “distanceZ” and “gyration” fail to have the PBC correction. For example, due to the membrane splitting the COM of the lipid bilayer lies in water, rather than lying inside the bilayer.

Can someone please suggest how PBC can be maintained on the CVs and this problem be corrected?

Thanking you

Malay Ranjan Biswal

Theoretical Science Unit
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Jakkur, Bangalore-560 064, India

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