May I ask which is the key word I should look up into, in order to print out
the decomposed energy terms of a static amber coordinate file? Thank you
very much!
Best,
Mo
On Wed, Oct 19, 2011 at 10:18 PM, Mo Chen <mc842.cornell.edu> wrote:
> 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 - 20:00:02 PDT
