On 6/6/17 8:22 AM, Mahboobeh Eslami wrote:
Hi all GMX usersI want to do MD simulation on protein-ligand complex. There are two calcium ions in the protein structure. These ions play an important role. In the equilibration step, should I consider protein,ligand and calcium ions as one single entity (for tc_grps option)? or should I consider these calcium as the part of ions in sol-ions group?ThanksBest
I consider structural ions to be part of the protein, not part of the bulk solution. -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.
