On 3/12/17 8:36 PM, Jonathan Saboury wrote:
Hello all, I generated a 3:1 POPE:POPG bilayer with charmm-gui, ran the minimization, equilibration, and production runs given. Then I copied the 10ns production run .gro to a different folder so that I can run it with charmm36-nov2016.ff instead of the ff given.
Why? The topology CHARMM-GUI gives you still works, and that's sort of the purpose - it gives you everything you need for the system.
When running the command "gmx_mpi pdb2gmx -ff charmm36-nov2016 -f old_membrane_lipid_only.pdb -o old_membrane_pdb2gmx.pdb -p topol.top -water tip3p" it generates a very large .top file (26.8 MB) that has [ atoms ] and perhaps other headings. I was under the impression that the .top should have been small and just contained the include line for where the POPE and POPG .itps were in the charmm36-nov2016. Did I do something wrong? Would this give me a simulation that isn't accurate?
No, because pdb2gmx will generate an explicit copy of the topology for every instance of every residue, which leads to an extremely redundant topology with many copies of lipids and water. As stated above, there is no need to re-generate your topology. Use what CHARMM-GUI gives you. We worked hard to make it easy for the end user :)
-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 [email protected] | (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 [email protected].
