Re: [AMBER] Implicit simulation

From: Jason Swails <>
Date: Wed, 30 Mar 2011 10:13:40 -0700

Implicit solvent doesn't typically use explicit counterions. If you're just
looking for elecrostatic screening, look at the saltcon variable for GB, or
istrng for PB.

If it turns out that you need explicit counterions for some reason, consider
using explicit solvent, or look carefully through the literature to see how
people have handled this case. Be prepared for careful validation of your
approach in this instance...

To actually answer the question, now: counterions are added via the
"addions" command documented in the manual.

Good luck,

On Wed, Mar 30, 2011 at 10:03 AM, Elisa Frezza <>wrote:

> Dear all
> I am performing an implicit simulation of a charged peptide linked to a
> porphyrin and I would like to include counterions.
> How can I do? How can I screen these charged residues?
> Thank you
> Elisa
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Wed Mar 30 2011 - 10:30:04 PDT
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