Re: Implicit solvent lipid bilayer simulation in NAMD.

From: Subbarao Kanchi (
Date: Wed Sep 17 2014 - 14:27:10 CDT

Hi Jason and Aron,
                                 I have read few recent papers where they
have been used the distance dependent dielectric constant model instead of
explicit solvent with CHARMM ff. But they have used the CHARMM md package.
I really want to know whether the distance dependent dielectric implemented
in NAMD and same time I am trying with the generalize born implicit


On Thu, Sep 18, 2014 at 12:24 AM, Aron Broom <> wrote:

> 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 <>
> wrote:
>> 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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