On 2/29/16 4:25 AM, Mahboobeh Eslami wrote:
dear Justin thanks for your answer I have another question. Which of the following items is better in mdp file for the equilibration and MD production steps? tc-grps = Protein-DNA SOL-ION or tc-grps = Protein DNA SOL-ION
Probably irrelevant if the protein and DNA are of reasonably large size. I would probably couple the complex together.
-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.
