Paper Citing NAMD - Abstract
Cooper, April M.; Kaestner, Johannes
Averaging Techniques for Reaction Barriers in QM/MM Simulations
CHEMPHYSCHEM, 15:3264-3269, OCT 20 2014
Herein, we test and compare different techniques to obtain averaged reaction barriers from quantum mechanics/molecular mechanics (QM/MM) simulations based on snapshots taken from molecular dynamics. Reasonable values can be obtained from a fairly small sample of well-chosen snapshots if an exponential averaging, also called Boltzmann averaging, is used. Snapshots with geometries close to the expected transition state are to be picked preferentially. Exponential averaging, arithmetic averaging, and simply taking the minimum barrier are compared to free-energy calculations from umbrella sampling. Three reactions within a protein in a water environment are used as test cases.
