Dear Amber users/developers,
May I ask how the "cut" functions in PMEMD facility? I have learned that
while running MD using CHARMM, we could specify ctonnb, ctofnb, so that the
switching function is turned on at the distance < ctofnb and > ctonnb in
calculating vdw energy, as well as the shifting is turned on in calculating
electrostatic energy. On the other hand, in Amber, I found we could define
CUT, or vdw_cutoff & es_cutoff when using PMEMD, in which CUT represents the
cutoff value. May I ask if the CUT in PMEMD is the same as ctofnb in CHARMM?
And is there a similar parameter of ctonnb in PMEMD? And if so how is it
defined? The parameter RGBMAX is set to be 25 as default? May I ask if this
is also related to any CHARMM parameter? Finally, may I ask what is the name
of the source code file that contain all these parameters? Thank you very
much!
Best,
Mo Chen
Graduate Student
Department of Food Science
Cornell University
Ithaca, NY 14850
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Received on Wed Oct 19 2011 - 19:30:03 PDT
