On Wed, Apr 13, 2011, Elisa Frezza wrote:
>
> I would like to ask you if I can perform MD simulation using implicit
> solvation model and a cubic box to confine my systems.
No: the implicit solvent models in Amber don't know about periodic
boundary conditions.
It might be possible to include a "solvent cap" (without solvent!) to confine
the systems, but the physics of this is very different than periodic boundary
conditions.
...regards...dac
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Received on Wed Apr 13 2011 - 10:00:06 PDT
