On Mon, Nov 27, 2017 at 2:30 AM, rose rahmani <rose.rhm...@gmail.com> wrote:
> > > On Mon, Nov 27, 2017 at 1:55 AM, Alex <alexanderwie...@gmail.com> wrote: > >> Hi, >> >> The answer is clearly in the error, just read it please: >> 2.848793 > 0.49 * (4/2) where 4 is the box length. >> >>> But i choose ( by pull_coord1_dim) Z direction for pulling (12 nm not >>> 4nm), it doesn't mean that protein should just get closer to ZnS(sheet) in >>> Z direction? >> >> thank you so much >> >> >> >> You can either keep the “pull_coord1_geometry = distance” and increase >> the box length or change the “pull_coord1_geometry” to “= >> direction-periodic“. I prefer the former though. >> >> Cheers, >> Alex >> >>> I've got it. >> >> would you please answer to another questions too? thank you in advance >> >> > >> >> >> On Sun, Nov 26, 2017 at 23:10 rose rahmani <rose.rhm...@gmail.com> wrote: >> >> > 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. >> > >> -- >> 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. > > > -- 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.