Hello i'm trying to do umbrella sampling and this is part of md_umbrella.mdp; DEFINE = -DPOSRES integrator = md dt = 0.001 nsteps = 40000000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 5000 nstenergy = 10000 nstxtcout = 10000 rlist = 1.5 coulombtype = pme rcoulomb = 1.5 vdwtype = Switch rvdw_switch = 1.0 rvdw = 1.2 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 ----------------- when i use grompp i get this erro and notes;
NOTE 1 [file md_umbrella.mdp, line 52]: md_umbrella.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. -------------------- Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.17# ERROR 1 [file md_umbrella.mdp]: With Verlet lists rcoulomb!=rvdw is not supported NOTE 2 [file md_umbrella.mdp]: Replacing vdwtype=Switch by the equivalent combination of vdwtype=Cut-off and vdw_modifier=Potential-switch ---------------- i used version 4.5.4 before grompp and i think this error comes from using gmx,but i dont know how EXACTLY should i change mdp file when i us gmx. (i want to move protein toward ZnS and protein is 1.5nm far from ZnS at t=0 and both of them are in center of simulation box at t=0). 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.