On 10/29/16 7:44 AM, Mijiddorj Batsaikhan wrote:
Dear Justin, Thank you very much for your all helps. (1) How can I easily reduce these clashes? Is there any good software?
You're using it. The point of energy minimization is to relax the structure. It just so happens that you have some nasty ones.
(2) from geometrical view, EM.gro structure looks fine. However, there are many individual protons separated from Lipid molecules. Is this usual?
Depends on the distance. Visualization software typically renders bonds based on assumptions about bond lengths. If the X-H bonds are actually longer than they should be, then your topology is probably wrong or the initial bad geometry caused distortion of the structure that couldn't be resolved. Typically, the result will be bad forces that do not converge below a sane tolerance, though.
-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.
