Daer AMBER Users,
I am quite confused behind the working principle of the 'lie' attribute
(Section 29.10.39, AMBER Manual 2018). It is clearly mentioned that for
each frame, it calculates the non-bonded interactions between all atoms
specified in <Ligand mask> with all atoms in <Surroundings mask>.
Electrostatic and van der Waals interactions are calculated for all atom
pairs. The electrostatic interaction is calculated with the Coulambic
shifting function provided along with.
However, I can't understand how the absolute values obtained from the Eelec
calculation can be exactly the Coulombic interaction energy when the error
function that is added to the direct sum cancels out with long-range term
solved in reciprocal space with the PME treatment (Cisneros, G. AndreĢs, et
al. "Classical electrostatics for biomolecular simulations." *Chemical
reviews* 114.1 (2013): 779-814.)? Please help to understand this.
Thanks,
B Manna
PhD Scholar
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Received on Thu Sep 20 2018 - 13:30:02 PDT
