Re: namdplot

Date: Thu Dec 09 2004 - 05:59:11 CST

Hi Vivek,

I can't really comment on your first question, since I have no experience
with NAMDplot. But as for constant-volume dynamics, well, basically that's
what you get unless you specifically use constant pressure. In other words,
if you don't invoke one of the NAMD options to use constant pressure, then
the size of your MD box will remain static, i.e., constant volume.

Of course, the concept of a "box" and a "volume" only make sense if you are
using some sort of periodic boundary conditions for your system...
you have a cluster of atoms surrounded by infinite vacuum....

So, just use one of the constant-temperature methods, along with periodic
boundaries (but without constant pressure) and you have NVT dynamics.

good luck,

C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania

Quoting vivek sharma <>:
> 2. Also I want to know is there a way to run NVT ensemble in NAMD, I see
> the
> methods and options for constant Temperature and constant Pressure, but
> not
> for constant volume. Please explain briefly.
> Thanking you,
> sincerely
> Vivek (NAMD newbie)

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:03 CST