Dear gromacs users, i ´ve beem trying to get the geometries of a drug molecule permeating an ion channel, the drug molecule is in a greater Z position than the Protein, but i always get the error :"Segmentation fault (core dumped)" this is my .mdp
title = Umbrella pulling simulation DOX ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 250000 ; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 cutoff-scheme = Verlet ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 20 ns_type = grid rlist = 1.2 rcoulomb = 1.2 rvdw = 1.2 ; 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 = Protein POPC Water_and_ions_DOX tau_t = 1.0 1.0 1.0 ref_t = 310 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 1.0 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_geometry = cylinder ; pull_vec1 = 0.0 0.0 1.0 ; pull_dim = N N Y pull_start = yes ; define initial COM distance > 0 pull_ngroups = 1 pull_group0 = Protein pull_group1 = DOX pull-r1 = 1.0 pull-r0 = 1.0 pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 800 ; kJ mol^-1 nm^-2 pull_pbcatom0 = 8485 According with other post, i have to select a pull_pbcatom0 closes to the middle of my reference ( an atom close to the middle of the ion channel's pore) and a pull_vec1 positive even if the drug is "above" the channel, i was wondering if you could help me with this, or giving me an advice of this error, thanks in advance Andrés Ortega -- View this message in context: http://gromacs.5086.x6.nabble.com/Umbrella-pulling-Drug-Ion-channel-tp5015363.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.