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 <[email protected]
<mailto:[email protected]>> 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
--
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