I honestly forgot why (took too long, erred, or both) so I tried to do charm-gui again. From my current attempt it is taking a while. I'm on the last step and I'll keep checking the output.
I'll keep you updated when something happens. Thanks again, your help is invaluable! - Jonathan P.S. I am seriously impressed on all the projects you are on and still have time to do user help XD On Sun, Mar 12, 2017 at 5:59 PM, Justin Lemkul <[email protected]> wrote: > > > 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]. > -- 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].
