Dear All, I'm running set of umbrella sampling simulations to get the PMF of a disaccharide binding to a protein. I followed the tutorial provided by Justin and changed the values of necessary parameters according to my system. The mdp file for umbrella sampling simulations is as follows: ------------------------------------------- ; Pull code pull = umbrella pull_geometry = distance ; can't get PMF with direction pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = active_site pull_pbcatom0 = 575 pull_group1 = new pull_pbcatom1 = 1500 pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 750 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps ----------------------------------------------------
Active site in the pull_group0 being the residues in the binding site and new in the pull_group1 being the disaccharide. Initially I did an SMD run where I separated the disaccharide from the binding upto 1.5nm in distance. When I started running the umbrella sampling simulations, I used the conformations with approximately 0.1nm difference starting from an initial separation of 0.3nm between the binding site residues and disaccharide. My question is: when I run g_wham and get the profile, the pmf reaches a plateau, but its not completely horizontal. It drops down a little. Is it acceptable to have the pmf reach a plateau but not completely horizontal? In the histogram, the first two windows have good overlap and are narrow distributions where as the later windows are spread out. I have tried to decrease the distance from 0.1 nm to 0.05 nm and still the sampling around 0.5-0.75 of Xi region does not sample well. Is there anything that you could suggest? I have uploaded the plots of profile and histograms. PMF Plot link: http://img801.imageshack.us/i/pmf.png/ Histogram link: http://img217.imageshack.us/i/histoy.png/ Thanks for your time Sai Ramadugu
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