Yes we should go back to the original approach that I put implemented when I
added it to Sander and PMEMD and had Wei put into Sleap. Why was this
changed??? Where was the rational and the discussion for changing it on the
AMBER dev mailing list?
There was a VERY good reason for setting the 1-4 scale factors for
additional dihedrals and impropers to zero. It is a safety check in the code
and people should not be messing with this!
Where are all the test cases guys? - Come on! Messing with leap is probably
the easiest place to hang us all so whoever updates it needs to be EXTREMELY
CAREFUL and test it extensively. A mistake here could end up wrecking
research for thousands of people and destroying ALL our reputations so I
urge you all to be extremely cautious and careful!
I do not want to discourage people, I am just trying to make you all
consider the consequences if you mess up.
All the best
Ross
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Friday, November 11, 2011 12:47 PM
> To: AMBER Developers Mailing List
> Subject: Re: [AMBER-Developers] significant recent tleap changes
>
> On Fri, Nov 11, 2011 at 3:34 PM, B. Lachele Foley <lfoley.uga.edu>
> wrote:
>
> > "I noticed that the *current* practice for adding 1-4 scaling factors
> into
> > the topology file is actually broken by the recent changes."
> >
> > You're talking just about the 1-4 scaling factors assigned to
> impropers?
> > Since, typically, none of those atoms is actually a "4" at all, does
> it
> > make sense to assign numbers? Do they just get ignored anyway?
> >
>
> They are *supposed* to get ignored. That was the rationale behind
> putting
> a 0 there. If they're really getting ignored, then those numbers are
> never
> used. However, if they are being used (when they shouldn't), the fact
> that
> you have 1/0 makes energies blow up. It's a fail-safe, as I understand
> it.
>
> My main question was should we put those back in?
>
> All the best,
> Jason
>
>
> > I just added "Make tleap tests" to my calendar. Will have some soon.
> >
> > :-) 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, November 11, 2011 2:54 PM
> > To: AMBER Developers Mailing List
> > Subject: [AMBER-Developers] significant recent tleap changes
> >
> > Hello everyone,
> >
> > I'm a little concerned about tleap and all the changes it's been
> seeing
> > recently (not that it's creating bad topologies, yet). The recent
> changes
> > have caused a small test failure in the NAB directory due to the new
> IPOL
> > additions. However, this alerted me to what I considered a rather
> > deficient tleap test suite. The current tests
> > ($AMBERHOME/AmberTools/test/leap) only test the creation of OFF
> library
> > files and old-style topology files(!) From the look of it, these are
> the
> > only tests we have for tleap, is this correct? (Except the indirect
> ones
> > like those in NAB).
> >
> > I created a test in the leap directory (added to the default test
> suite) to
> > create an amber7 style topology (solvated and GB-ready) using an
> AmberTools
> > 1.5 (fully patched) version of tleap. I noticed that the *current*
> > practice for adding 1-4 scaling factors into the topology file is
> actually
> > broken by the recent changes. The behavior we discussed in
> > http://dev-archive.ambermd.org/201108/0000.html is no more (impropers
> no
> > longer get 0's, they get 1.2/2.0).
> >
> > Do we want to go back to the original behavior (which would require
> adding
> > some of Arunima's original code back in) or just live with the new
> version?
> >
> > Thanks!
> > Jason
> >
> > P.S. -- Another note -- A topology file created prior to the 1-4
> scaling
> > addition in tleap actually differed quite a bit from the topology
> file
> > created after the 1-4 scaling feature patch was added. It appeared
> under
> > slightly-more-than-just-skimming scrutiny to be a slight
> rearrangement of
> > some dihedral pointers, but I didn't do an exhaustive check. In any
> case
> > it'll be nice to be able to trace tleap changes through a more
> extensive
> > test suite (I don't think what I added was sufficient, but better
> than
> > _nothing_).
> >
> > --
> > 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
> >
>
>
>
> --
> 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
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Received on Fri Nov 11 2011 - 16:00:03 PST
