Thank you Justin for your help. On Wednesday, March 9, 2016 6:38 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 3/9/16 1:42 AM, mohammad r wrote: > Thank you Parham and Justin, Excuse me I have another question, in simulation > of a water-peptide system, is it necessary to use QM/MM simulation during the > entire process? Because I didn't see it in the tutorials. By the way I > generated the pdb file by using charmm-gui then import it in amber to get the > topology and coordinate files, finally I converted the topology and > coordinate files to gromacs format and did the rest of simulation by gromacs. > but I didn't run QM/MM simulation. Does it make trouble in the results? The technique(s) used depend on the scientific question(s) being posed before doing the simulations. If you expect some reactions, etc. to be taking place, then you need QM/MM. If you just want to simulate a peptide over time, then plain MD is fine. Methodological details like this should be decided long before one approaches a keyboard :) -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.