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

[devicerandom]

On 14/12/10 18:35, Bob Johnson wrote:
> Can anyone answer this question or guide me somewhere with helpful
> information?
> Thanks,
> Bob

I was going to send a very similar mail -namely, I have a coarse-grain 
system in vacuum where I'd like to simulate a charged polymer. My idea 
was that of adding a single "ghost" counter-ion with zero VdW 
interactions, perhaps keeping it fixed in one corner of the box, but I'd 
like to know how meaningful it is.

thanks!
m.

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