[gmx-users] difference in potential energy

[Justin Lemkul]

On 8/30/17 6:24 AM, Emran Heshmati wrote:
> Thanks to mark for his explanations.
> We performed MD simulation on a peptide fragment as well as its mutants
> where, its residues have been systematically replaced by alanine residue.
> We found that potential and kinetic energies of one mutant (T=>A) is
> significantly different from other molecules. interestingly there are other
> similar substitutions in different positions indicating that molecules with
> similar masses and chemical formula are being compared. apparently, we are
> facing with an special case in which the changing of the position of a
> residue has profound effect on the kinetic and potential energies. our
> question is related to the interpretation of this finding!!

You're taking a larger residue and making it smaller, also eliminating 
hydrogen bonding by making the residue nonpolar. Kinetic and potential 
energies are extrinsic properties, so all you're likely seeing is a 
reflection of the fact that you've changed the size of the residue.  
Neither quantity is a free energy, which is what is actually useful.  
Your results might be completely different if you use a different force 
field, for instance.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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