[gmx-users] Re: gb_saltconc in implicit water simulations

[Bob Johnson]

Can anyone answer this question or guide me somewhere with helpful
information?
Thanks,
Bob

On Thu, Dec 9, 2010 at 4:52 PM, Bob Johnson <bobjohnson1981 at gmail.com>wrote:

> Hello everyone,
> I am trying to use implicit solvent with a CG DNA model. The model,
> however, uses explicit charges, which means that the DNA carries an overall
> negative charge. When using implicit solvent with a charged system in other
> codes (e.g. Amber), the electrolyte is taken care of implicitly as well.
> However, in Gromacs this is currently not implemented since gb_saltconc is
> always set to 0. Without any salt, the DNA duplex is obviously unstable. Are
> there plans on implementing implicit counterions so that one can set
> gb_saltconc to nonzero values?
>
> It doesn't seem natural to include explicit counterions to neutralize the
> system when using implicit solvent. Is there a typical protocol one follows
> to neutralize charged systems when using implicit solvent?
> Thanks,
> Bob
>
> --
> Bob Johnson, PhD
> Institute for Computational Molecular Science
> Temple University
> 1900 North 12th Street
> Philadelphia, PA 19122
> http://astro.temple.edu/~rjohnson <http://astro.temple.edu/%7Erjohnson>
>



-- 
Bob Johnson, PhD
Institute for Computational Molecular Science
Temple University
1900 North 12th Street
Philadelphia, PA 19122
http://astro.temple.edu/~rjohnson
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