Re: Implicit solvent lipid bilayer simulation in NAMD.

From: Jason Swails (
Date: Wed Sep 17 2014 - 13:47:53 CDT

On Wed, Sep 17, 2014 at 2:41 PM, Subbarao Kanchi <> wrote:

> Hi Siva,
> Thank you for the reply. I read the namd manual and you are
> correct it is not compatible with PME. I have not used the PME in my input
> file.

​I don't see how GB can possibly work for lipid bilayer simulations. The
only lipid simulations I've seen in recent work has used a periodic unit
cell (and normally long-range electrostatics, like PME or RF or something).

For one thing, GB represents an infinitely dilute system (since the solvent
goes out to infinity in all directions and you have a finitely countable
number of lipid molecules). Under such experimental conditions, you would
expect the bilayer to _eventually_ dissolve and dissociate, so this
approach seems doomed from the start (at least to me).

For another thing, I'm not aware of any efforts to parametrize GB models
for lipids -- probably because it wouldn't work well regardless of model

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher

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