On 8/7/14, 8:47 AM, Meenakshi Rajput wrote:
Thank you Justin. Please tell me if emtol should be 1000 or 100 for albumin
There are no hard and fast rules when running normal MD simulations.
protein complex? As for emtol=1000, complex(mentioned in the tutorial) is converged in some steps and graph plotted for potential energy shows sudden downfall. Please tell me what is the reason behind this?
If there is a dramatic decrease in energy, there should be an obvious structural change somewhere. Watch the trajectory.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
