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
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> AMBER-Developers.ambermd.org
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Received on Tue Dec 20 2011 - 15:00:02 PST
