Why not do two umbrella sampling simulations: one with initial conformations from your faster pulling and one with initial conformations from your slower pulling. Then you can run them both as regular US simulations until (a) neither US PMF is drifting systematically with increasing simulation time and (b) they converge to the same answer. This way, you might also be able to make some comment on the relative importance of doing the initial pulling slowly.
Next time, please wait until your post has appeared on the list (it is currently awaiting approval for inclusion of large images) before sending me a private email asking me to comment on-list (which is, by itself, fine with me). Also: I can't make heads or tails of your plots. (i) I have no idea which one corresponds to which force constant; (ii) you mentioned 4 force constants but you posted 8 figures; (iii) I can not read any of the axes or labels. Chris. ________________________________________ From: surampu...@gmail.com [surampu...@gmail.com] Sent: 29 July 2013 19:39 To: chris.ne...@utoronto.ca Subject: Umbrella sampling question Hi Chris, I have seen many of your contributions to the Umbrella sampling topic in the forum. It would be of immense help to me if you can throw light on a few points. I am running my first umbrella sampling simulation, and having hard time to decide if the PMF plot I am getting is right or wrong. I am pulling one atom from a short polymer chain from the center of a micelle and trying to obtain a PMF plot along the distance from the center of the micelle to the surface and eventually few nanometers away from the micelle. Here is the mdp file for the pulling: title = Umbrella pulling simulation define = -DPOSRES_surfpoly ; Run parameters integrator = md dt = 0.002 ; timestep (ps) tinit = 0 nsteps = 250000 ; 500 ps= 0.5ns nstcomm = 10 ; remove COM every 10 steps ; Output parameters nstxout = 5000 nstvout = 5000 nstfout = 250 nstxtcout = 250 nstenergy = 500 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = System tau_t = 0.5 ref_t = 300 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella ; COM pulling using umbrella potential between reference group and other groups ;pull_geometry = distance ; simple distance increase pull_geometry = direction ; simple distance increase ;pull_dim = Y N N ; pulling in x-direction pull_vec1 = 1 0 0 ; pulling in x-direction pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 ; we are only applying a pulling force to one group pull_group0 = surf ; reference group for pulling pull_group1 = poly ; group to which pulling force is applied pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 300 ; kJ mol^-1 nm^-2 I have repeated pull run using various force constants (pull_k1=300,500,1000,2000 kJ/mol/nm^2) to pull over 5 nm distance with 0.1nm windows and none of them is a clear pick as in the tutorial as to which one to use for umbrella sampling. From my understanding, force constant should neither be too low or too high. Is there a simpler way to decide which one is the right force constant to use from the plots? Please see the link below for the F vs time and position vs time plots (top to bottom order --- pull_k1=2000, 1000, 500, 300 kJ/mol/nm^2). http://gromacs.5086.x6.nabble.com/Umbrella-sampling-force-vs-time-plots-tp5009709p5010097.html Thanks a lot, Andy S. _____________________________________ Sent from http://gromacs.5086.x6.nabble.com -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
