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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Received on Fri Aug 16 2013 - 18:30:03 PDT
