Re: [AMBER-Developers] NTB

From: Yong Duan <>
Date: Tue, 20 Dec 2011 14:12:25 -0800

Great! I like it.

Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
On 12/20/11 2:03 PM, "Jason Swails" <> wrote:
>Hello everyone,
>I implemented an idea I had about
> (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
>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
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Received on Tue Dec 20 2011 - 14:30:09 PST
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