Re: Does GB Implicit Solvent handle explicit ions?

From: Gianluca Interlandi (
Date: Sun Apr 17 2011 - 22:43:37 CDT

If you are using an implicit solvation model, you don't need to neutralize
the system. Neutralizing the system is something that you really need only
with periodic boundary conditions (in particular with PME), where the
system (protein+bulk) is replicated in all three space directions to avoid
finite size effects. Since with an implicit solvation model you don't have
this problem, you can skip the ionization process.

However, some GB implicit solvent models take the ionic strenght
implicitly into account. I don't know whether NAMD's GB model does. But in
any case, I wouldn't worry about neutralizing the system with explicit


On Sun, 17 Apr 2011, David Tanner wrote:

> I don't have an answer, but here is a paper which partially addresses that question.
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> David E. Tanner
> Theoretical and Computational Biophysics Group
> 3159 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> On Apr 17, 2011, at 12:30 AM, marawan hussain wrote:
> HI David,
>  i want to know how can i neutralize by adding ions prior to submission to MD run using the
> implicit solvation model in NAMD 2.8. Do i need to solvate first then neutralize by ions
> addition then remove the water molecules and submit to the MD run using the implicit
> solvent model or this implicit solvation model can handle the unneutralized
> (charged)protein.
> Thanks
> Marawan

Gianluca Interlandi, PhD
                     +1 (206) 685 4435

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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