Can anyone answer this question or guide me somewhere with helpful information?<br>Thanks,<br>Bob<br><br><div class="gmail_quote">On Thu, Dec 9, 2010 at 4:52 PM, Bob Johnson <span dir="ltr"><<a href="mailto:bobjohnson1981@gmail.com">bobjohnson1981@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hello everyone,<div>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?</div>
<div><br></div><div>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?</div>
<div>Thanks,</div><div>Bob</div><div><br>-- <br>Bob Johnson, PhD<br>Institute for Computational Molecular Science<br>Temple University<br>1900 North 12th Street<br>Philadelphia, PA 19122<br><a href="http://astro.temple.edu/%7Erjohnson" target="_blank">http://astro.temple.edu/~rjohnson</a><br>
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</blockquote></div><br><br clear="all"><br>-- <br>Bob Johnson, PhD<br>Institute for Computational Molecular Science<br>Temple University<br>1900 North 12th Street<br>Philadelphia, PA 19122<br><a href="http://astro.temple.edu/~rjohnson">http://astro.temple.edu/~rjohnson</a><br>