On 9/29/14 10:09 AM, Sathish Kumar wrote:
Dear gromacs usres, I have run the umbrella sampling with the help of tutorial of justin....In my system rna is binding with gold nanoparticle...to find out the binding energy i run the umbrella sampling using the space 0.2 nm and i got total 59 configurations, each configuration was run for 5 ns. The profile files are shared with the link below. https://www.dropbox.com/s/c8tj2rhu620xkim/Slide1.JPG?dl=0 https://www.dropbox.com/s/745kixwrfvguyyt/Slide2.JPG?dl=0 In the profile image, i have not got the plateu value, can i take the difference between final and starting pmf values for the binding enrgy. Please give suggestions.
You don't have either a plateau or a defined minimum, so I'd say that the reaction coordinate is incomplete, either in terms of the sampling within the windows or the window setup itself.
-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.
