Water Sphere

From: Raul Araya Secchi (arayasecchi_at_hotmail.com)
Date: Mon Oct 24 2005 - 15:21:27 CDT

Dear NAMD Users:

Im triying to perform an alchemical FEP calculation to asses the effect of a
mutation in the binding free energy of a protein-protein complex but I dont
want to put the whole complex into a water box and use Periodic Boundary
Conditions, because it will make my calculations to slow. So I was wanderin
how can I put a sphere of water arround the interaction interface and keep
the rest of the protein with harmonic constrains and a dielectric constant
to replace the slovent.

Thanks

Raul Araya
Center for Genomics and Bioinformatics
Catholic University of Chile
Santiago
Chile

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