Re: Fwd: Water Box size

From: Philip Blood (
Date: Fri Feb 10 2006 - 13:37:54 CST

Are you doing anisotropic pressure coupling (useFlexibleCell set to
yes)? This may result in these kinds of changes in box dimensions. For
a water box you should have the pressure control coupled in each
direction (useFlexibleCell set to "no").


snoze pa wrote:

> Dear NAMD community,
> I am doing my simulatin at NPT. My simulation is going fine till
> heating. ut for Free MD simulation My water box size is increasing in
> one direction. While the postion of the protein remain same. I don't
> know what is wrong with this? I am also attaching after 1ns simulation
> protein and waterbox snapshot.Here are two snapshot
> 1. namdmin.png for after minimization
> 2. namd1ns.png is after 1ns free run.
> I don't know why my water box size is increasing in one direction.
> thanks in advance
> snoze
> ------------------------------------------------------------------------
> ------------------------------------------------------------------------

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:36 CST