[gmx-users] difference in potential energy

Emran Heshmati compbioph at gmail.com
Wed Aug 30 12:24:43 CEST 2017

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!!

On Sun, Jun 25, 2017 at 2:45 AM, Emran Heshmati <compbioph at gmail.com> wrote:

> Dear Gromacs users
> I performed alanine scaning mutagenesis using gromacs on a peptide
> fragment consisting 16 aa. In one of the mutations, the kinetic energy of
> the system was significantly different. How can I interpret this result?
> any comment is welcome
> regards
> Emran

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