Will upload to dropbox later (strict 'no external cloud' institutional policy). I don't know if the tpr is completely self-contained, so please let me know if you need the ff folder as well.
Thank you, Alex On Wed, Nov 1, 2017 at 4:42 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > We have had several reports of "lost particles while sorting" but we would > like a .tpr on an issue on redmine.gromacs.org to be able to investigate, > please! > > Mark > > On Wed, Nov 1, 2017 at 10:19 PM Alex <nedoma...@gmail.com> wrote: > > > Hi all, > > > > I am using walls in the cowboy mode, GMX v. 2016.3, system is a porous > > membrane (periodic in XY) with water and ions -- everything works fine > with > > pbc=xyz and no walls. With walls, mdrun throws "Software inconsistency > > error: Lost particles while sorting." > > > > mdp exerpt below: > > > > pbc = xy > > nwall = 2 > > wall-type = 12-6 > > wall-r-linpot = 0.0 > > wall_atomtype = opls_996 opls_996 > > wall-ewald-zfac = 3 > > periodic_molecules = yes > > ns_type = grid > > rlist = 1.0 > > coulombtype = pme > > ewald-geometry = 3dc > > fourierspacing = 0.135 > > rcoulomb = 1.0 > > rvdw = 1.0 > > vdwtype = cut-off > > cutoff-scheme = Verlet > > > > This uses a custom type "opls_996" properly defined in ffnonbonded of the > > FF (custom OPLSAA). Any suggestions? I can provide more info, if needed. > > > > Thank you, > > > > Alex > > -- > > 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.
