On 5/6/16 3:32 AM, Rishikesh Parulekar wrote:
Hi, I have completed simulation for 10ns and while analysing the trajectories through UCSF chimera i encountered that for some time my protein structure is getting distorted (pulled to other side from original confromation). Because of this I am getting fluctuated RMSD. My input parameters for md.mdp are same as mentioned in the bevan lab tutorial. What could be the possible reason ??
With Google you would have gotten an answer in seconds, rather than hours... http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -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.
