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 <bobjohnson1...@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
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
