[gmx-users] Fw: minimization for final configuration
dear Justin thanks for your replyThe plot of the RMSD against time for the trajectory generated with g_rms shows a maximum RMSD about 0.195 nm. I set cut-off value to 0.2 nm for g_clusters command. Is it a appropriate value?Sincerely.On Tuesday, September 30, 2014 2:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/30/14 3:36 AM, Mahboobeh Eslami wrote: hi GMX users i have simulated the protein-ligand complex by gromacs for 20ns. The average for the final structure of 18 to 20 nanoseconds has been achieved.is minimization for the final average structure required?Sincerely. An average structure might be totally unphysical. Energy minimization of an unphysical structure leads you to something that is probably useless. I'd suggest doing clustering if you're interested in the predominant conformation(s) during a certain time period of the simulation. -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.
Re: [gmx-users] Fw: minimization for final configuration
On 9/30/14 9:58 AM, Mahboobeh Eslami wrote: dear Justin thanks for your reply The plot of the RMSD against time for the trajectory generated with g_rms shows a maximum RMSD about 0.195 nm. I set cut-off value to 0.2 nm for g_clusters command. Is it a appropriate value? g_rms and g_cluster do different types of RMSD evaluation. g_rms compares against a single reference structure, g_cluster does RMSD between frames to decide on clusters, so the output of g_rms is not necessarily an indicator here. You can tell for yourself whether or not the value was suitable by inspecting the loads of output that g_cluster provides you, and by visualizing the contents of the clusters to ensure that structures that were clustered together are reasonably similar. For a structure that doesn't change much, you'll probably get one really big cluster and then a few that are sparsely populated. -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.
