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 Sincerely, Thomas On Saturday, November 8, 2014 7:05 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 11/8/14 6:53 PM, Thomas Lipscomb wrote: > Dear gmx-users, > > I am still following this tutorial: > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html > > > But I got an error at this step: > "Note how many lipids were deleted and update the [ molecules ] directive of > your topology accordingly. Run energy minimization. Then, scale down the > lipids by a factor of 0.95 (assuming you have used default names, the result > of the minimization is called "confout.gro"): > perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 > area_shrink1.dat" > > > [tlipscomb@prime-radiant KALP]$ perl inflategro.pl confout.gro 0.95 DPPC 0 > system_shrink1.gro 5 area_shrink1.dat > Eeeeek! No confout.gro at all! > As the error says, the file "confout.gro" does not exist. Either (1) you named it something else, (2) energy minimization failed for some reason, or (3) it's somewhere else on your file system. -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. -- 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.
