Ok I am further along, now at: "Follow this up by another round of EM. During the "shrinking" steps, be sure to change the cutoff value to 0, or else you will continue to delete lipids! After 26 iterations of scaling down by 0.95, I reached an area per lipid of ~71 Å2, above the experimental value of ~62 Å2. Since the script tends to overestimate the area per lipid, this value is good enough to continue to equilibration."
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html My best guess on how to do that is this: /usr/local/gromacs/bin/gmx grompp -f minim.mdp -c confout.gro -p topol_dppc.top -o em2.tpr /usr/local/gromacs/bin/gmx mdrun -s em2.tpr -v (THIS IS THE SECOND ENERGY MINIMIZATION) plus some perl commands Because I'm repeating what I did before: /usr/local/gromacs/bin/gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr /usr/local/gromacs/bin/gmx mdrun -s em.tpr -v I'm having trouble figuring out how to do 26 iterations Sincerely, Thomas On Saturday, November 8, 2014 7:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: 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.
