Re: [AMBER-Developers] Zero VDW radii causing havoc.

From: Scott Le Grand <varelse2005.gmail.com>
Date: Fri, 16 Aug 2013 20:57:53 -0700

What values do you use for A and B?
On Aug 16, 2013 7:34 PM, "B. Lachele Foley" <lfoley.ccrc.uga.edu> wrote:

> I can only add the reminder that our main workaround has been to increase
> the size of the water box. That is, it disproportionately seems to affect
> smaller systems. The locals who run simulations of really large systems
> never seem to see this. Sure, they can't run as long, but there are many
> more interactions in each step. I suspect most lipid simulations are also
> much larger than some of the systems we run. I can't promise that this
> information is useful, but there it is.
>
> FWIW, we're going to re-run some simulations that failed, but with our HO
> vdW terms on the HW, just to see what happens.
>
> We haven't seen it in CPU. I realize that doesn't mean it couldn't happen
> there.
>
> :-) Lachele
>
> Dr. B. Lachele Foley
> Complex Carbohydrate Research Center
> The University of Georgia
> Athens, GA USA
> lfoley.uga.edu
> http://glycam.ccrc.uga.edu
>
> ________________________________________
> From: Ross Walker [ross.rosswalker.co.uk]
> Sent: Friday, August 16, 2013 10:02 PM
> To: AMBER Developers Mailing List
> Subject: Re: [AMBER-Developers] Zero VDW radii causing havoc.
>
> Scott, I'm still not sure I am convinced on this being the issue. We have
> many many simulations done with TIP3P water - probably hundreds of
> milliseconds in aggregate, a lot with boosted potentials and other types
> of enhanced sampling and haven't seen this issue. Sure we've seen problems
> with zero VDW hydroxyl hydrogens before - but those are always when they
> are constrained to be close to each other or with massive attraction such
> as in some sugars and phosphates. I don't think I've ever seen problems
> with TIP3P before since the bonds are rigid and the H's are, I believe,
> inside the VDW sphere of the oxygen. Hence I would never expect to see
> this for two waters, for a water and a strained hydroxyl perhaps but even
> then unlikely.
>
> Are you certain this is a real problem and not a strange artifact, and or
> subtle bug? - Do we have any repro's for the CPU code?
>
> The only place I'd expect there could be problems with TIP3P is if it is
> run without shake. So something must be unique about the examples here
> that are showing the repro that doesn't normally occur in protein and/or
> dna simulations.
>
> Ps. we've never seen a problem with the lipid12 force field as far as I
> know and we have over 100 microsecs of simulation on these systems.
>
> Hence I am still a little suspicious...
>
> All the best
> Ross
>
>
>
> On 8/16/13 6:20 PM, "Scott Le Grand" <varelse2005.gmail.com> wrote:
>
> >Yep, that's why I moved the bug over to pmemd and away from pmemd.cuda...
> >
> >
> >
> >
> >On Fri, Aug 16, 2013 at 6:17 PM, B. Lachele Foley
> ><lfoley.ccrc.uga.edu>wrote:
> >
> >> We only had one, the HO (Ho) term. It's been made non-zero which at
> >>least
> >> fixed the issue in the highly charged, perfectly aligned situation
> >>where we
> >> first saw it. BTW, we (specifically Matt) first observed it on CPU.
> >>
> >> Can changing the LJ A term like that potentially mess up other things
> >>like
> >> hydrogen bonding?
> >>
> >> :-) Lachele
> >>
> >> Dr. B. Lachele Foley
> >> Complex Carbohydrate Research Center
> >> The University of Georgia
> >> Athens, GA USA
> >> lfoley.uga.edu
> >> http://glycam.ccrc.uga.edu
> >>
> >> ________________________________________
> >> From: Scott Le Grand [varelse2005.gmail.com]
> >> Sent: Friday, August 16, 2013 9:11 PM
> >> To: AMBER Developers Mailing List
> >> Subject: Re: [AMBER-Developers] Zero VDW radii causing havoc.
> >>
> >> There are a heck of a lot more TIP3P waters running around your test
> >>case.
> >> Anything with an effective zero VDW radius is a problem.
> >>
> >> 20 years ago, I used to see these when I did global conformational
> >>search
> >> of proteins. And when it happened, energies would plummet into a deep
> >> abyss and hose the search process. The only thing different with MD is
> >> that the finite timestep messes up a water badly enough that the fast
> >>Shake
> >> recovers it into a bizarre position that now hits a bunch of other atoms
> >> and then all you-know-what breaks loose and we're off to NaNdyland...
> >>
> >> The more things change...
> >>
> >>
> >> On Fri, Aug 16, 2013 at 6:06 PM, B. Lachele Foley <lfoley.ccrc.uga.edu
> >> >wrote:
> >>
> >> > Jason said: "The problem-case hydrogens in the relevant carbohydrates
> >> > (and lipid?) force fields should be modified if they represent
> >>problems
> >> in
> >> > normal simulation. "
> >> >
> >> > FYI: Scott Le Grand, in the bug report Ross mentioned, just said it
> >>was
> >> > two TIP3P waters doing it.
> >> >
> >> > :-) Lachele
> >> >
> >> > Dr. B. Lachele Foley
> >> > Complex Carbohydrate Research Center
> >> > The University of Georgia
> >> > Athens, GA USA
> >> > lfoley.uga.edu
> >> > http://glycam.ccrc.uga.edu
> >> >
> >> > ________________________________________
> >> > From: Jason Swails [jason.swails.gmail.com]
> >> > Sent: Friday, August 16, 2013 3:28 PM
> >> > To: AMBER Developers Mailing List
> >> > Subject: Re: [AMBER-Developers] Zero VDW radii causing havoc.
> >> >
> >> > On Aug 16, 2013, at 11:39 AM, David A Case <case.biomaps.rutgers.edu>
> >> > wrote:
> >> >
> >> > > On Fri, Aug 16, 2013, Ross Walker wrote:
> >> > >
> >> > >> So I am proposing that we have code in rdparm that detects zero VDW
> >> > radii,
> >> > >> prints a warning message about it and then adjusts these radii in
> >>the
> >> > code
> >> > >> to 0.0000001.
> >> > >
> >> > > I don't understand how/why this fixes any problem. First, you would
> >> have
> >> > > to get to distances comparable to the radius for such a term to have
> >> any
> >> > > effect. You would have already very much messed things up by that
> >> point.
> >> > > Second, atoms like OH have a zero epsilon as well as a zero radius,
> >>so
> >> > > just changing the radius would have no effect.
> >> >
> >> > I think Ross meant changing the A and B coefficients to 1E-6 or so,
> >>not
> >> > the pre-combined values.
> >> >
> >> > I'm with Dave on this though. I've run many microseconds of net
> >> simulation
> >> > and I've never seen a problem with zero vdW terms in HO atom types. I
> >> > realize there are some cases where this bug hits you, but as I recall
> >>it
> >> is
> >> > a strange case with carbohydrates. I'm wary about just making these
> >> changes
> >> > under the assumption it will have only remedial effects. The
> >>problem-case
> >> > hydrogens in the relevant carbohydrates (and lipid?) force fields
> >>should
> >> be
> >> > modified if they represent problems in normal simulation.
> >> >
> >> > I can also quite easily write a quick parmed action to implement these
> >> > changes without having to hard-code this new convention immediately
> >>into
> >> > every md engine we have.
> >> >
> >> > Also, I think that the amber codes should implement the Amber force
> >>field
> >> > exactly as it is defined in the prmtop. Implicitly changing
> >>parameters in
> >> > the MD codes is a bad idea, IMO. (How hard would it have been to
> >>validate
> >> > chamber if CHARMM took that approach?) So if we decide to implement
> >>this
> >> > change, it should be done in LEaP, not rdparm (but again, I think the
> >>LJ
> >> > terms should be derivable straight from the combining rules).
> >> >
> >> > > Note that Istvan's lmodprmtop hack directly changes the LJ A term
> >>from
> >> > > zero to 1000. This has the advantage of not assuming any particular
> >> > mixing
> >> > > rules, i.e. it still works when NBFIX like changes have been used.
> >> >
> >> > As an aside, should lmodprmtop functionality be incorporated into
> >>parmed
> >> > and/or cpptraj if it does simple things? (I'm not sure what else it
> >> does...)
> >> >
> >> > All the best,
> >> > Jason
> >> >
> >> > _______________________________________________
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> >> > AMBER-Developers.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >> >
> >> >
> >> >
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> >> >
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Received on Fri Aug 16 2013 - 21:00:03 PDT
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