[gmx-users] gb_saltconc in implicit water simulations

[Bob Johnson]

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
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