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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