From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
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.
Jerome
On 10 July 2017 at 15:17, Malay Ranjan Biswal <malay_at_jncasr.ac.in> 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
> http://www.jncasr.ac.in
>
>
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