[gmx-users] Lost particles while sorting

Mark Abraham mark.j.abraham at gmail.com
Fri Nov 3 02:18:30 CET 2017 

Hi,

On Fri, Nov 3, 2017 at 2:11 AM Alex <nedomacho at gmail.com> wrote:

> Hi Mark,
>
> It may be a good idea for you guys to document walls a bit better than
> what we have right now. What was happening became clear to me pretty
> quickly, but the error text is kinda obscure and the documentation on
> walls is brief. :)
>

Granted. There's a bajillion ways for a newcomer to any simulation type to
shoot themselves in the foot. Where would be a good place for "with walls,
set up your simulation cell so the initial positions of all the particles
are on the correct side of the wall?"

I am encountering more unexpected things with walls, e.g. rather strong
> E-z not having any effect on ions -- still preliminary though. I suppose
> this will probably need another thread if I confirm it, but do you have
> any recollection of anything specific to walls + external fields? Yes, I
> am indeed trying to separate the ionic population. ;)
>

That combination is one of the very large number of things in GROMACS that
I know very little about. But a new topic might get the interest of any who
do know!

Mark

Thanks,
>
> Alex
>
>
> On 11/2/2017 6:11 PM, Mark Abraham wrote:
> > Hi,
> >
> > 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. ;-)
> >
> > Mark
> >
> > 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.
> >>
> >> Alex
> >>
> >>
> >> 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
> >> 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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> >>>>>
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