Hi, On Fri, Nov 3, 2017 at 2:11 AM Alex <nedoma...@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 <nedoma...@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 <nedoma...@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 <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? 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