On 11/8/14 7:35 PM, Thomas Lipscomb wrote:
Ok so the tutorial did not give me the energy minimization command I have to find it and execute it before I can do perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat The manual has 3 different types to choose from: 3.10 Energy Minimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 3.10.1 Steepest Descent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 3.10.2 Conjugate Gradient . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 3.10.3 L-BFGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 I'm sorry but I don't know what to do. The good news is that I already have minim.mdp
The membrane tutorial is considered somewhat advanced, as I don't spell out exactly what to do. As the introduction states, it assumes you are familiar with what "run energy minimization" would mean. If you have a suitable .mdp file, you have coordinates, and you have a topology...that's all you need to run grompp.
-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.
