The change was made to both during the commit. I think it's worthwhile to
make all behavior common between the programs where their functionalities
overlap.
All the best,
Jason
On Tue, Dec 20, 2011 at 5:53 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Jason,
>
> Great work. Looks good to me. Can you also make this behavior the same in
> pmemd as in sander so they remain consistent?
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Jason Swails [mailto:jason.swails.gmail.com]
> > Sent: Tuesday, December 20, 2011 2:03 PM
> > To: AMBER Developers Mailing List
> > Subject: [AMBER-Developers] NTB
> >
> > Hello everyone,
> >
> > I implemented an idea I had about
> > http://dev-archive.ambermd.org/201112/0001.html (regarding NTB). It
> > encapsulates the desired behavior of those wanting to do away with the
> > variable altogether while at the same time allowing users access to all
> > the
> > functionality they have now if they insist they want it. A nice
> > side-effect is that this should not break any input files anybody has
> > laying around.
> >
> > Effectively what is done is the default value for NTB becomes dependent
> > on
> > other input variables.
> >
> > If NTP > 0 --> NTB == 2
> > If IGB > 0 --> NTB == 0
> > Otherwise, NTB == 1
> >
> > Any specified value overrides this default for NTB, but except in
> > (very)
> > weird circumstances, NTB can effectively be completely ignored.
> >
> > Likewise, I made the CUT default dependent on whether we're doing a
> > periodic simulation (eqv to NTB > 0), in which case the value is 8 as
> > per
> > usual, or an implicit solvent/igb=6-vacuum calculation, in which case
> > the
> > default is 9999. Again, any specified value for CUT overrides these
> > defaults, so it really shouldn't impact anybody's existing input files
> > (since cut==8 with igb > 0 is a fatal error in sander/pmemd right now,
> > anyway). I think Bob wanted to do this in pmemd, since he had all the
> > machinery in place to set different CUT defaults, but ultimately
> > decided
> > that compatibility with sander was more important.
> >
> > The Amber11.lyx file was appropriately updated for this.
> >
> > Thoughts? These changes are easily unrolled by reversing 3 commits,
> > but I
> > thought I'd get this out there for review (or thrashing, whichever)
> > before
> > the impending code freeze.
> >
> > Thanks!
> > Jason
> >
> > --
> > 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
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Received on Tue Dec 20 2011 - 17:00:03 PST
