The BONDS_INC_HYDROGEN, BONDS_WITHOUT_HYDROGEN tables have an integer index into parameter tables BOND_FORCE_CONSTANT, and BOND_EQUIL_VALUE.
How aggressively should the bond parameters be coalesced with duplicate parameters being coalesced into one?
Aggressive coalescence will give smaller bond parameter tables but may not run as fast because of poor cache behavior when the dynamics code is running?
One set of parameters for every bond will give larger parameter tables but might run faster?
My guess is that aggressive coalescence is better.
Do any Amber developers have strong feelings one way or the other?
Christian Schafmeister
Professor, Chemistry Department
Temple University
meister.temple.edu
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Received on Sat Sep 24 2016 - 07:00:02 PDT
