From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Mon Sep 10 2018 - 11:53:13 CDT
The cutoff used in the QM/MM code in NAMD is the same as the cutoff
defined for non-bonded interaction in the classical calculation, so
changing that value will change the cutoff for both MM non-bonded
interactions and QM/MM point charge determination.
All QM codes we used so far take some sort of point charge information in
order to run their calculations in an electrostatic embedding. your
question regarding the cutoff is very pertinent, and all I can tell you is
that it will depend on the error you tolerate. One of the methods used to
reduce the error of a hard cutoff is applying a smoothing function of the
point charges (which NAMD provides, with several options). Another one is
to simply increase the cutoff and allow the natural 1/r part of the
potential do the smoothing for you (some people add *all* of the classical
system in their QM calculations).
In this field, it is hard to find one recipe for all applications, but I
hope this helps.
--- Marcelo Cardoso dos Reis Melo PhD Candidate Luthey-Schulten Group University of Illinois at Urbana-Champaign crdsdsr2_at_illinois.edu +1 (217) 244-5983 On Wed, 5 Sep 2018 at 10:22, Agisilaos Chantzis <agisilaos.chantzis_at_gtn.ai> wrote: > Dear all, > > > In the QM/MM implementation of NAMD it is documented that in the > electrostatic embedding of QM part an effective cutoff radius is used > (rmax) to decide which MM partial charges will be included in the QM > calculations. What I could not really find documented is how this cutoff > is chosen and whether it can be modified so as to asses it's influence > on the accuracy of the calculations. Since the long range electrostatic > interactions should not be abruptly cut in general, how is the use of > this rmax cutoff justified in the description of the electrostatic > environment of the QM part? > > > Sincerely, > > > Agisilaos Chantzis > >
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