On 12/1/13 9:39 AM, shahab shariati wrote:
Dear Justin Thanks for your reply If I place drug molecule within the water, can I use the same Pull code parameters in the case drug molecule within lipid bilayer? pull = umbrella pull_geometry = position ; simple distance increase pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = CHOL_DOPC pull_group1 = drg pull_rate1 = 0.001 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 100 ; kJ mol^-1 nm^-2 pull_init1 = 0 pull_vec1 = 0 0 1
Try it and see. The settings depend on where you place everything. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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.