Complete Beginner

From: Philip Peartree (
Date: Mon Aug 20 2007 - 07:38:30 CDT


I am just starting out using NAMD, but I have been using Charmm31 for 2
years. A
lack of speed has enforced the switch, but I am unsure on a couple of
things. I
have read the ubiquitin tutorial, and that has helped with a great many
but there are still a few things I don't quite understand.

1. Is there a recommended procedure for performing M.D. with NAMD, i.e.
timescales for heating, equilibration.
2. With my Charmm simulations I have been heating with harmonic constraints on
the protein, and then gradually relaxing them throughout the equilibration
stage, is this appropriate, and if so, how can I achieve a change in
temperature. I assume it's via tcl scripting, but I cannot find anywhere that
says how to achieve this.
3. Are there any "Gotcha's" I should watch out for, I've been caught by
ones in Charmm and this has delayed my work quite significantly.

Thanks, and sorry if this is quite a simplistic question!

Philip Peartree
Computation Molecular Enzymology Group
University of Manchester

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