On 12/27/13, 6:00 PM, Ali Alizadeh wrote:
Dear All users, I have a question about calculation of potential energy for an especial group. I know I had to define an energy group in .mdp file. I forgot to do it. I want to know can I extract this potential energy by post processing or not? If not this means I must perform my simulation again?
There is no .mdp option to calculate the potential energy of just a single group. One can excluded nonbonded interactions between pairs of groups or decompose nonbonded energy between pairs of groups.
One could obtain "the potential energy of a group" by stripping out the coordinates of interest from the original trajectory (with trjconv), making a matching .tpr file (with tpbconv), then recalculating energies with mdrun -rerun. Such a quantity would be useless, though.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. 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 ================================================== -- 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.