[gmx-users] Lost particles while sorting

[Alex]

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.abraham at 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 <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
> 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
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