Re: Maintaining PBC on Collective Variables

From: Vermaas, Joshua (
Date: Mon Jul 10 2017 - 12:49:11 CDT

Hi Malay,

There are two options I've tried, one is just to add z-restraints to
selected lipid atoms. This prevents the membrane from moving too far so
it doesn't split, and has the benefit of not needing to be repeated. The
other option is to occasionally recenter the restart file so that the
coordinates remain centered on the membrane before the PBC box is split.
Ideally, what would happen is that the colvars routine can be told to
specify a specific atom or group as the center of the PBC cell, rather
than using NAMD's box center, but I don't think this is in the cards yet.


On 07/10/2017 07:25 AM, Jrme Hnin 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

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