Ok - so I tried a few tests this evening and I think the conclusion is that
either:
1) PMEMD CUDA works fine for OPLS.
2) AMBER has NEVER implemented OPLS correctly.
Sadly I think I have to go with 2 - but then I don't think anybody has ever
actually implemented OPLS correctly and 2 actually in this case implies 1 is
fine - as in pmemd.cuda implements the broken opls the same as sander and
pmemd.
Attached are the test cases. Specifically I did:
$AMBERHOME/tleap -f buildit
where buildit is:
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Tuesday, May 29, 2012 11:49 AM
> To: AMBER Developers Mailing List
> Subject: Re: [AMBER-Developers] [AMBER] manual prmtop file editing for
> free energy calculation
>
> On Tue, May 29, 2012 at 4:54 AM, David A Case
> <case.biomaps.rutgers.edu>wrote:
>
> > On Mon, May 28, 2012, Ross Walker wrote:
> > >
> > > Out of interest how does Leap know to use different combining rules
> for
> > > OPLS?
> >
> > The "AC" vs. "RE" flag in the non-bonded section triggers a change in
> > combining rules. (I think! check the code or run a simple test
> > calculation.)
> >
>
> This isn't going to help my case, but I don't see where this happens.
> mathop.c, line 69 (function MathOpConvertNonBondToAC). This only
> appears
> to satisfy the Amber combining rules. That function itself is only
> called
> in two places in unitio.c (and nowhere does it look like we try to
> match
> "RE" or "AC"). So unless I'm missing something, OPLS just gets the
> Amber
> combining rules inside tleap...
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Wed May 30 2012 - 00:00:03 PDT
