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