What (change in) free-energy difference are you trying to measure? How do these potential energy (differences) relate to them?
Mark On Sat, Jun 29, 2013 at 7:13 PM, Leandro Bortot <leandro....@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
