On 5/9/14, 9:38 AM, mirko busato wrote:
Dear Justin, Thank you very much for your quick reply, In my .mdp file I set up energygrps to protein ITA. (ITA is the group for the Itaconic acid monomers) After that I tried to launch g_energy command on .edr file. Is it right? which energy terms do you suggest me to use for my problem (to understand the affinity peptide-monomer)?
The short-range nonbonded terms are the only ones that get decomposed in a pairwise fashion, so the new terms should be fairly obvious from the screen output.
Whether or not those numbers mean anything is another story; they may give you some insight into the enthalpic driving forces, but they tell you nothing of the actual free energy of binding.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
