From: Tim Isgro (timisgro_at_ks.uiuc.edu)
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.
Tim
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
>
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