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

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Tue Mar 03 2009 - 00:05:58 CST

Hi Marie -

To add to what Peter has already written, keep in mind that covalent
bonds in a typical namd simulation will not break as this is a
function of how namd reads the topology and forcefield for
calculations. What you will see at different temperatures is
increased mobility at higher temperatures, but it is best to define
some standard structural parameter to measure to quantify this. For
example, you can analyze the rmsd of the backbone atoms. However, I
believe that for most simulations, a higher temperature will increase
mobility and encourage denaturation. Perhaps a measurement such as
change in solvent accessible surface area would be a better measurement.

-Eric

On Mar 2, 2009, at 11:37 PM, Peter Freddolino wrote:

> 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
>>

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

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