Re: Implicit solvent lipid bilayer simulation in NAMD.

From: Aron Broom (
Date: Wed Sep 17 2014 - 13:54:57 CDT

I think if you wanted to simulate how a protein for instance might behave
if entirely constrained within a bilayer, but without actually using the
lipids, there may be some work being done to develop implicit solvent
methods where the solvent is a lipid-like thing (dissolving your protein in
hexane for instance).

There may also have been some success with using coarse-grained methods for
doing things with lipid layers (particularly I think the NAMD supported
MARTINI forcefield has been used for this), if you are trying to save on
performance from the necessarily massive systems one gets when solvating a
big bilayer patch.

On Wed, Sep 17, 2014 at 2:47 PM, Jason Swails <>

> 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
> parameters.
> Good luck,
> Jason
> ​
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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