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

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Mar 02 2009 - 23:37:11 CST

Hi Marie,
potential energies are independent of temperature, and since those are
what namdenergy measures, you will not see different results when
analyzing a trajectory. You would need to actually run your simulation
at different temperatures to see any effect.
Hope this helps.

Peter

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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