Dear Amber users:
Does anybody know what energies are given in the sander (pmemd) output
when the ibelly=1 option is used? After some experimenting, I figured
only the moving-moving atom interactions are included, not the
fixed-fixed; I am not sure about the moving-fixed ones.
But in the dynamics, my understanding from the manual saying: "Note
also that this option (belly) does not provide any significant speed
advantage...", is that all energies are calculated (thus, no speed
advantage).
Also, if belly is used during thermodynamic integration, what energies
are involved in the dvdl output? The same as above? Or is it
implemented differently than above?
Thanks so much for your help,
Ignacio
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Received on Tue Jul 26 2011 - 07:30:03 PDT
