[gmx-users] Lost particles while sorting
mark.j.abraham at gmail.com
Fri Nov 3 01:11:16 CET 2017
Yes that seems consistent with some theories Berk had when we chatted over
lunch. Specifically, if the linear potential is too weak then you wouldn't
get the repulsion you seek. Clearly you've found some other more basic ways
that a system preparation protocol would not have respected the intended
effect of that wall.
BTW there is a "private" mode on Redmine that I hope normal users can use
in cases where they have systems whose details they would like to keep to a
small group of need-to-know types. That will work better than getting lost
in my inbox. ;-)
On Thu, Nov 2, 2017 at 11:29 PM Alex <nedomacho at gmail.com> wrote:
> So, I have a bit of an update -- hopefully this will somewhat help others
> encountering this error, because it may not be entirely a bug...
> 1. The issue can be overcome by first and foremost not applying walls to a
> system previously run without any -- that was my mistake and it makes
> physical sense. Dynamic equilibration has to be performed with walls and
> corresponding pbc setting. This, however, does not guarantee anything if
> the system is e.g. solvated -- that is, if there are atoms expected very
> close to walls, or beyond them. In addition, if there atoms looking for
> neighbors across the box (through previously set pbc), that can be
> catastrophic. See below.
> 2. After solvating, but before EM, reinsert the system in a box slightly
> larger in the z-direction. For a box initially 4 nm long in Z in my case,
> reinserting in a 4.6 nm long box worked here.
> 3. Particles seem to be lost when wall-r-linpot is set improperly, so try
> various values (0.25 nm worked for me).
> 4. The entire concept here is naturally very messy. I could think of
> optional functionality, which allows for removing entire molecules whose
> atoms are anticipated to be beyond walls, or close enough to result in
> local explosions. However, that is also messy and can be done manually in
> previous steps, so no elegant suggestion from my end, unfortunately, other
> than being very mindful when setting this up.
> On Wed, Nov 1, 2017 at 6:26 PM, Alex <nedomacho at gmail.com> wrote:
> > Mark,
> > Could you please share your email address, so I can send you the tpr
> > privately? I don't want this work to be public just yet, if that's okay.
> > Thanks,
> > Alex
> > On 11/1/2017 4:42 PM, Mark Abraham wrote:
> >> Hi,
> >> We have had several reports of "lost particles while sorting" but we
> >> like a .tpr on an issue on redmine.gromacs.org to be able to
> >> 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
> >>> FF (custom OPLSAA). Any suggestions? I can provide more info, if
> >>> Thank you,
> >>> Alex
> >>> --
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