Hi when calculating an energy contribution using g_energy, the units specified in the plots, as well as in the output tables, are kJ/mol. This happens even when the -nmol flag is missing (so nmol=1). On the other hand, the energy units in gromacs are kJ/mol. So I guess that when a term (a dihedral or whatever) is added to the total potential it refers to kJ per mol of that term. The total energy of a system comes from the sum of all the potential energy plus the kinetic energy contributions and the units are again kJ/mol. Then, how should I understand that? kJ per mol of system contained in the unit cell?
Let me put an example: I have 6 solute molecules solvated in 5000 SPC waters and I use g_energy to determine the coulombic contribution to the solute-water interactions or to the solute-solute interactions as a function of time. The result is given in kJ/mol. If I want to determine the same contribution(s) per mole of solute should I divide by 6 maintaining the units as kJ/mol? Then, if I have the same system with 12 solute molecules, would make sense to compare the equivalent contribution divided by 12? After taking a look to the code and to the results for a couple of systems I think this is correct but the answer is too basic and important just to assume that I am right so I would be happy if I have a confirmation. Thanks in advance, Ángel. -- 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
