Thanks for all your considerations on this subject! I guess I must review the some of the underlying concepts.
Regards, Manel -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: 2 de abril de 2014 21:23 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] drug-drug interaction energy On 4/2/14, 12:23 PM, Manuel Azenha wrote: > Dear all, > > > > When I simulate a solution of a drug in water/methanol to study the > self-aggregation, and try to determine the interaction energy between > the drug molecules , I'm getting net positive values whatever the > drug. I'm simply defining the drug groups in .mdp. Should it be > entered some other way ? How do those energies compare to the drug-water or drug-methanol energies? Remember that a pairwise nonbonded interaction energy is not a free energy. If you used PME, the value returned by energygrps isn't even fully accurate because the mesh term is not decomposed. The magnitude of the effect probably depends on the size of the molecules being considered and the distance over which they interact. -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. -- 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.
