[AMBER-Developers] NTB

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 20 Dec 2011 17:03:27 -0500

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.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Tue Dec 20 2011 - 14:30:08 PST
Custom Search