On Apr 8, 2013, at 10:39 AM, Syed Tarique Moin <tarisyed.yahoo.com> wrote:
> Hello,
>
> I am interested to simulate a protein in implicit solvent with periodic boundary condition. Can someone suggest me is it possible in Amber.
No. This is a highly unusual calculation. Periodic boundary conditions are used to avoid surface effects in explicit solvent simulations. Since implicit solvent simulations do not have solvent boundaries (the continuum goes on forever), there is rarely a reason to use periodic boundary conditions.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 08 2013 - 13:30:02 PDT
