Hi,
You can add ions to your system using the 'addions' command from tleap:
addIons unit ion1 numIon1 [ion2 numIon2]
In your case of course ion1 and be Na+ and ion2 Cl-. You can choose
numion1 and numion2 to fit whatever concentration you need. See the
AmberTools manual for full details on the 'addions' command. Hope this
is helpful.
-Dan
On Fri, Oct 28, 2011 at 5:01 AM, Beale, John <John.Beale.stlcop.edu> wrote:
>
> I am simulating a small protein in explicit water. I would like to do a dynamics experiment simulating the effects of a low concentration of sodium chloride in the water. Does Amber-11 offer a way to do this? Thanks!
>
> John Beale
>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Fri Oct 28 2011 - 04:30:03 PDT
