On 1/10/15 3:52 PM, mah maz wrote:
Dear all, I wanted to know if the potential energy gained by "g_energy -f ener.edr -o" the total potential energy of the system or partial ones like vdw energy. If it is the total energy, to my knowledge it should be negative,
It's the full potential energy. Various components are also printed out to the various energy terms printed by g_energy.
and its summation with the kinetic energy should be negative showing the stability of the system. In my simulation, potential energy is positive and the total energy is a big positive number, but no explosion happened. What is the problem?
That depends entirely upon what your system is. A negative potential is generally expected for most condensed-phase systems, in which attractive nonbonded interactions dominate over repulsive terms. But the energy of a given system is entirely dependent upon what the system is.
-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.
