On 11/8/14 8:52 PM, Thomas Lipscomb wrote:
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
You don't need topol_dppc.top for anything except making DPPC whole. Ignore those files after you've accomplished this.
It boils down to understanding what InflateGRO is suppose to do. Once you start compressing/shrinking the lipids, you minimize after each step and compress some more. So you minimize the output of shrink step 1, which is then input into InflateGRO to shrink again (shrink2), minimized, input into InflateGRO...
-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.
