Dear all,
I'm performing an umbrella sampling simulation on an ion pulled from the bulk of a phase1 to the COM of a phase2 (taken as reference) along the z-axys in a biphasic system to calculate the PMF related to the transfer from phase1 to phase2. The box is 3.62 X 3.62 X 7.24 nm and the interphase is more or less at z = 3.62 nm. This is the pulling part of the .mdp file for the pulling simulation: ; Pull code pull = umbrella pull-ngroups = 2 pull-group1_name = Other pull-group2_name = zn pull-geometry = distance pull-coord1-groups = 1 2 pull-ncoords = 1 pull-dim = N N Y pull-coord1-rate = -0.02 pull-coord1-k = 1000 pull-start = yes 36 configurations have been chosen to cover a path from the bulk of phase1 (distance with COM of phase2 = 3.4 nm) to the COM of phase2. Each configuration was equilibrated for 5 ns and then simulated for 10 ns in NPT conditions (298.15 K, 1 atm). This is the pulling part of the .mdp file for the NPT simulation of each configuration: ; Pull code pull = umbrella pull-ngroups = 2 pull-group1_name = Other pull-group2_name = zn pull-geometry = distance pull-coord1-groups = 1 2 pull-ncoords = 1 pull-dim = N N Y pull-coord1-rate = 0.0 pull-coord1-k = 5000 pull-start = yes refcoord_scaling = com In addition to the umbrella potential, position restraints of 2000 KJ mol-1 nm-2 on the x and y-axes have been applied to the ion to prevent movement on the xy-plane. This is the obtained PMF profile: https://ibb.co/hj9je6 and these are the histograms: https://ibb.co/cYssXR I was wandering: 1) why the PMF curve doesn't reach a plateau when the ion is in the middle of the phase1, i.e. for d close to zero. Could it depend on the simulation time or should I build a bigger box so that the ion is sorrounded by a larger amount of phase1? 2) why I get those little jumps on the plateau from d = 2.5 nm to d = 3.4 nm (ion close to the middle of phase 1). The histograms seem to be quite well overlapped. Thank you in advance for your answers Kind regards, Matteo Busato -- 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 [email protected].
