On 11/26/13 11:48 PM, Mahboobeh Eslami wrote:
Hi Dear Gmx Users, Do not just following procedure can be usedby gen_vel: NVT gen_vel = yes gen_temp=300 gen_seed=-1 NPT gen_vel=no MD gen_vel=no i want to study the changing of velocity in md stage. Can I use the following method: NVT gen_vel = yes gen_temp=298 gen_seed=-1 NPT gen_vel=no MD gen_vel = yes gen_temp=298 gen_seed=-1
I don't understand what purpose this serves. If you re-generate velocities after equilibration, what was the purpose of equilibration in the first place? You trash the previous ensemble, and depending on the algorithms you're using for temperature and pressure coupling, you run the risk of simply crashing the simulation. If you're looking for better sampling through independent trajectories (from different initial velocities) the first approach does that just fine.
-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.