From: Chris Harrison (char_at_ks.uiuc.edu)
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 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 On Mon, Mar 2, 2009 at 11:32 PM, Marie N <onenumbernut_at_yahoo.com> 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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