[AMBER] periodic boundary condition

From: juan zeng <azengjuan.gmail.com>
Date: Wed, 14 Apr 2010 17:34:40 +0800

Dear amber users:
          I want to calculate the binding affinity on protein-ligand complex
with the linear interaction energy method,in this environment the binding
affinity comprises Van der waals interaction potential and electrocstatic
interaction potential.while others used the non-periodic boundary condition
to calculate the binding affinity ,now I wish that this calculation can be
done in the periodic boundary condition.because the molecules in cell far
away from the center cell will interaction with the protein-ligand complex
in the center cell,so I need to find out a method that can calculate the
interaction energy(especially the electrostatic interaction energy) of the
complex with all other molecules in the whole simulation system.Can you give
me some suggestion how to make this calculation be realized.
        Hope receive your reply.

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Received on Wed Apr 14 2010 - 03:00:02 PDT
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