On 8/1/17 10:01 AM, Alex Mathew wrote:
Dear all gromacs users, I would like to build a protein-membrane system to perform umbrella simulation; I need to calculate the molecule transportation by pulling it from top to bottom. In the tutorial, it says "Some force fields include everything you need. For instance, it is unwise to try to literally follow this approach for a force field like CHARMM36, as it needs no modification. In that case, you are much better off building the system with CHARMM-GUI <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/www.charmm-gui.org> . I want to use Charmm36 force field, but I did not see any option to make a box for US (as mentioned in US tutorial). Any suggestion how should I proceed?
Specify large enough box dimensions in whatever direction you want (probably z) when building the box. There's no specific "build a system for umbrella sampling" because the only consideration unique to this case is the box size.
-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.
