[gmx-users] g_energy units

Mark Abraham mark.j.abraham at gmail.com
Sat Jun 29 20:24:44 CEST 2013

What (change in) free-energy difference are you trying to measure? How
do these potential energy (differences) relate to them?


On Sat, Jun 29, 2013 at 7:13 PM, Leandro Bortot <leandro.obt at gmail.com> wrote:
> 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
> kJ/mol.
>      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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