Re: Minimization with CHARMM

From: Tim Isgro (
Date: Mon Feb 09 2004 - 17:04:13 CST

Hi Ted,

Here is an input script that beginners may find helpful. It contains a
lot of options which you may not need, but gives a feel for how the NAMD
commands should be implemented. Note that sections preceded by 'if{0}{'
will not be interpreted as part of the script, while 'if{1}{' sections
will. This way you can use a single script for many simulations, turning
on/off options as you need them.

> but the minimization
> doesn't appear to work that well

Are you minimizing for long enough? Check the post I just made to Gerald.


On Sat, 7 Feb 2004, ted q wrote:

> Hi,
> I'm a new user of NAMD and am trying to create/find a simple configuration
> file to minimize a PDB structure with the CHARMM potential. I already have
> downloaded the potential and have a very basic script, but the minimization
> doesn't appear to work that well, and I suspect it's because my parameters
> are non-optimal - could someone suggest a decent script to start out with?
> Thanks!
> -Ted
> ---------------
> Ted Quon
> Research Assistant
> University of Waterloo
> _________________________________________________________________
> The new MSN 8: advanced junk mail protection and 2 months FREE*

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:20 CST