Dear Users My umbrella sampling simulations are of 1 ns time whereas Dr. Lemkul's tutorial advocates a 10 ns simulation time. I found that after running WHAM , my histograms are coarser ( rough) compared to Dr. Lemkul's. A few of my histograms have two peaks!! So should I increase the simulation time from 1 ns to 10 ns ?? I do a 100 ps NPT equilibration and then a 1 ns umbrella sampling in each of my windows. The generated PMF curve is also not smooth and is discontinuous at one position which I think I can fix by adding more windows around that co-ordinate.
A picture is linked : HISTO <https://docs.google.com/file/d/0B-U8uULVZjfRQXcyUkI2bXhBcVE/edit?usp=drive_web> Kindly help. Thanks & Regards Agnivo Gosai Grad Student, Iowa State University. -- 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.
