Hi Justin, I have one general and one specific question about doing the pulling simulation. Can you let me know how I should choose pull_coord1_geometry among distance, direction, and cylinder? How can I distinguish these three geometries to use them in different systems? How can different choices affect the outcome (PMF curve)? Which methos you recomment to pull a molecule acroos the bilayer? why?
In my case, I want to calculate the permeability of ion in a specific bilayer. I faced this error: Can not have dynamic box while using pull geometry 'direction-periodic' (dim z) I found you already replied the similar issue: *"align the system such that you are pulling along z, in conjunction with semi-isotropic coupling and zero compressibility along z."* Can you explain how I should do that alignment in my pull code? This is my pull code: title = Umbrella pulling simulation define = -DDPPC_O ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 500000 ; 1000 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; continuing from NPT ; Single-range cutoff scheme cutoff-scheme = Verlet nstlist = 20 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 = MEMB SOL_ION tau_t = 1.0 1.0 ref_t = 303.15 303.15 ; Pressure coupling is on pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 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 pull_ncoords = 1 ; only one reaction coordinate pull_ngroups = 2 ; two groups defining one reaction coordinate pull_group1_name = CAL pull_group2_name = DPPC_O pull_coord1_type = umbrella ; harmonic potential pull_coord1_geometry = distance ; simple distance increase pull-geometry = direction-periodic pull_coord1_dim = N N Y pull_coord1_groups = 1 2 pull-coord1-vec = 0 0 1 pull-coord1-init = 0 ; pull_coord1_start = yes ; define initial COM distance > 0 pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 Your attention is highly appreciated. -- 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.