[gmx-users] g_energy units

Leandro Bortot leandro.obt at gmail.com
Sat Jun 29 19:13:49 CEST 2013

Dear users,
     is the energy output from g_energy really in kJ/mol?

     As an example, I wanted to know which isoform of a protein forms the
most stable dimer. I calculated the potential energy of the interaction
between two monomers of the dimer and I got -2000 kJ/mol for one isoform
and -4000 kJ/mol for the other.

     Shouldn't it be J/mol?
     If these values are really in kJ/mol, how can I interpret it in terms
of "molecular scale"? -2000 or -4000 kJ/mol sure is a lot of energy for
such scale, in which the energies are typically at the order or 10s of
     I know I'm not accounting for the entropic effects, but I have never
seen an entropy contribution in the scales of 1000 kJ/mol either...
     Is it the case as these energy values are somewhat arbitrary and I can
only say that one isoform has 2x the interaction energy of the other?

     I know this is not a "bad structure with high energy" case. I have
been wondering about the values from g_energy for quite a long time and I
have seen it in many different systems.

     my calculation procedure was as follows:
          From a standard explicit solvent MD trajectory (md.trr) I
extracted only the protein with trjconv, creating the file md_protein.trr.
I used tpbconv to do the same with the md.tpr file, creating
md_protein.tpr. Then I re-ran the MD over this trajectory with mdrun: mdrun
-s md_protein.tpr -rerun md_protein.trr -deffnm protein. The potential
energy of the dimer was extracted from the created protein.edr file. The
same was made for both chains A and B using an index file created with
make_ndx. The dimer interaction energy was calculated as "Potential_AB -
(Potential_A + Potential_B)".
          Is this wrong?

     Any help would be greatly appreciated.

Thank you in advance,
Leandro Bortot

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