I agree with Jason, but one effect is that you have infinite dilution. For
binding, you could use a flat well distance restraint to enforce a specific
concentration in a spherical volume.
On Apr 8, 2013 4:13 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>
>
> 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 - 14:00:03 PDT
