Re: Maintaining PBC on Collective Variables

From: Jérôme Hénin (
Date: Mon Jul 10 2017 - 08:20:55 CDT

You can't let your bilayer get split across the PBCs. Two options:

- disable wrapping
- prevent vertical diffusion by restraining the center of mass of the
bilayer along the z axis with a distanceZ coordinate. If you do that, use
few atoms, eg. one per lipid. You don't even need to restrain all lipids.

I would also try the zeroMomentum option, which should be sufficient to
prevent overall diffusion in the first place.


On 10 July 2017 at 15:17, Malay Ranjan Biswal <> wrote:

> 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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:25 CST