[Chimera-users] Potential Energy Calculations

Elaine Meng meng at cgl.ucsf.edu
Sat Sep 22 10:38:50 PDT 2012

Hi Nikolay,
There are a lot of levels to this question -- I hesitate to get into it, because it could be very complicated (and it's not a Chimera question per se).  

Concerns are why you want to calculate this quantity and whether it has any physical meaning.  If you are trying to calculate a solvation energy, there are many well-established computational approaches involving MD or MC simulations, or continuum dielectric calculations.   What you describe is only for a single configuration, without sampling or entropy considerations.

I would recommend thinking carefully about what quantity you are calculating, how it relates to any real property, and then investigating in the literature (or computational chemistry textbooks), on the web, and by questions to email lists such as CCL how best to proceed in terms of calculations.  Probably to get helpful answers from email lists, you should give some rationale, and solicit suggestions about your strategy as well as what programs to use to execute that strategy.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 21, 2012, at 8:33 PM, Nikolay Igorovich Rodionov wrote:

> Hi Elaine, 
> I posted my question on the ccl mail server, but I have one more question
> for you. I realize that this might be entirely appropriate for this
> mailing list but regarding my previous proposal, what if I modify the
> method to create 3 files.
> One file will be with just the protein, one with the solvated protein, and
> one it just the water molecules isolated from the solvated model. If I
> calculate the net energy in the each system, and then subtract the net
> energies of the protein only and water only systems from the net energy of
> the protein & water system, shouldn't this leave me with just interaction
> energy?
> I was also thinking about putting all of the water molecules into an
> energy minima orientation in both files with water by first running the
> minimization function in the file with water & protein, and then isolating
> the water molecules and writing them into a separate PDB for the
> water-only file since the energy minima orientation will change based on
> the environment. 
> Thanks for pointing me to a great resource by the way.
> Nikolay Rodionov

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