[gmx-users] Lost particles while sorting
nedomacho at gmail.com
Wed Nov 1 23:47:53 CET 2017
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.
On Wed, Nov 1, 2017 at 4:42 PM, Mark Abraham <mark.j.abraham at gmail.com>
> 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,
> On Wed, Nov 1, 2017 at 10:19 PM Alex <nedomacho at 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
> > 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
> > --
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