Hi; This is md_pull.mdp
integrator = md dt = 0.001 nsteps = 2000000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 500 nstenergy = 1000 nstxtcout = 1000 rlist = 1.5 rcoulomb = 1.5 rvdw = 1.2 coulombtype = pme cutoff-scheme = group vdwtype = Switch rvdw_switch = 1.0 pcoupl = no gen-vel = yes gen-temp = 0 gen-seed = 173529 constraints = h-bonds pbc = xy freezegrps = WAL ZnS freezedim = Y Y Y Y Y Y energygrp-excl = WAL WAL ZnS ZnS energygrps = SOL WAL ZnS Protein NA CL nwall = 2 wall-atomtype = C C wall-type = 9-3 wall-density = 150 150 wall-ewald-zfac = 3 ewald-geometry = 3dc fourierspacing = 0.12 tcoupl = v-rescale tc-grps = System tau-t = 0.1 ref-t = 300 pull = yes pull_ngroups = 2 pull_ncoords = 1 pull_group1_name = ZnS pull_group2_name = Protein pull_coord1_type = umbrella pull_coord1_geometry = distance pull_coord1_groups = 1 2 pull__coord1_dim = N N Y pull_coord1_rate = -0.001 ; 1 nm per ns pull_coord1_k = 5000 pull_coord1_start = yes Program gmx grompp, VERSION 5.1.4 Fatal error: Distance between pull groups 1 and 2 (2.848793 nm) is larger than 0.49 times the box size (2.000000). You might want to consider using "pull-geometry = direction-periodic" instead. the box size is= 4 4 12 could you please help me to resolve it? ----- Mr.Lemkul told me rcutt-off is wrong and i should'nt put "cutoff-scheme = group" >>>but when i remove it i'll get this error too; >>With Verlet lists rcoulomb!=rvdw is not supported i know it's wrong solution but what is my alternative?!! ------ -dummy particle should move towards the surface with a constant speed of 1 nm/ns from z = 2 nm to z = 0 and drags the CM by the harmonic force corresponding to the spring constant of 5000. I DON'T know how should i implement deltaZ(=2)? which .mdp option refers to it?! thank you so much Best regards Rose -- 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.
