Re: Simulation question

From: Paul Rigor (uci-ics) (
Date: Tue Jan 19 2010 - 18:29:03 CST

I'd say use box and make sure that you add enough padding (12A) beyond the
cutoff points for the non bonding forces setting. Your system will
essentially be calculating lots of H2O interactions but that avoids the
protein from "seeing its own image". Like every system, you'll have to
tweak as you go!


On Tue, Jan 19, 2010 at 9:26 AM, snoze pa <> wrote:

> Dear NAMD users,
> Please suggest me which approach is better to start a SMD
> simulation. Water in BOX or Water in Sphere?
> Thank You.
> S

Paul Rigor
Pre-doctoral BIT Fellow and Graduate Student
Institute for Genomics and Bioinformatics
Donald Bren School of Information and Computer Sciences
University of California, Irvine

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