Re: help running NAMD energy at multiple stable temperatures (newbie)

From: Chris Harrison (
Date: Wed Mar 04 2009 - 11:12:52 CST


Are you referring to bonds like Carbon-Carbon, Carbon-Nitrogen, etc bonds?
Or are you referring to hydrogen bonds?


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078
On Mon, Mar 2, 2009 at 11:32 PM, Marie N <> wrote:
> Hey,
> I am a junior in high school doing a  research project on prion proteins.
> I'm trying to analyze the effects of temperature on the bonds of the prion
> protein by running NAMD simulations at different temperatures. I am setting
> the temperature in the namdenergy.tcl file (I was not able to make a config
> file work). However, my energy results are the same for all temperatures.
> I'm using the most current version of VMD with the NAMD energy plugin.
> Am I setting the temperature correctly or is there something else I should
> be doing?
> Thanks for any help,
> Marie Nielsen

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