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