Dear AMBER users and devs,
I've come across something which seems slightly troubling. We interface
with both AMBER and NAB to obtain the energy, gradient and in the case of
NAB, the analytic second derivatives of the potential for the purposes of
locating transition states. As part of this process, we sometimes call NAB
followed by AMBER for the same coordinates.
In vacuum (igb=0) we get consistent energy and gradient from AMBER and NAB,
but when using igb=5, we get a completely different energy and gradient for
identical coordinates. Even more confusingly, although they are consistent
for igb=2 with the default external dielectric constant, if we set
extdiel=1, igb=2 also gives inconsistent energy and gradient. This is
summarised in the attached pdf.
I was wondering if one of the devs could comment on this. It appears that
igb=5 must be somehow implemented differently in AMBER and NAB, and
separately that the effect of extdiel is also different between AMBER and
NAB.
Thanks,
Chris
--
*Dr Chris Whittleston 栗主*
Department of Chemistry
University of Cambridge
Lensfield Road, Cambridge, CB2 1EW
Email: csw34.cam.ac.uk
Tel: +44 (0)1223 336423
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Received on Tue May 21 2013 - 09:00:03 PDT
