On 2/22/16 10:03 PM, Ming Tang wrote:
Thanks Justin, How about LJ and Coulomb energy? I want to see the trend of protein energy only. I defined 2 energy group: protein and SOL in .mdp file. Then, I saw LJ and Coulomb: protein-ptrotein option when using g_energy. Are they VDW and Coulomb force within the protein only?
The "protein energy" usually tells you nothing. Unless you're doing a more rigorous calculation like MM/PBSA, I wouldn't try to base anything off of these quantities. They're not free energies and they're totally force field-dependent results. From your previous post, I'm assuming you're using GROMOS96, which, while parametrized against free energies of solvation, does not guarantee that such short-range interaction energies actually correspond to something physically useful (unlike, e.g. CHARMM, which is directly parametrized against QM water interaction energies).
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
