Reproducing Quantum Probability Distributions at the Speed of Classical Dynamics: A New Approach for Developing Force-Field Functors

Abstract

Modeling nuclear quantum effects is required for accurate molecular dynamics (MD) simulations of molecules. The community has paid special attention to water and other biomolecules that show hydrogen bonding. Standard methods of modeling nuclear quantum effects like Ring Polymer Molecular Dynamics (RPMD) are computationally costlier than running classical trajectories. A force-field functor (FFF) is an alternative method that computes an effective force field that replicates quantum properties of the original force field. In this work, we propose an efficient method of computing FFF using the Wigner-Kirkwood expansion. As a test case, we calculate a range of thermodynamic properties of Neon, obtaining the same level of accuracy as RPMD, but with the shorter runtime of classical simulations. By modifying existing MD programs, the proposed method could be used in the future to increase the efficiency and accuracy of MD simulations involving water and proteins.

Ab Initio Molecular Dynamics Simulation and Energetics of the Ribulose-1,5-biphosphate Carboxylation Reaction Catalyzed by Rubisco: Toward Elucidating the Stereospecific Protonation Mechanism

“…However, in light of the results of the present computational study, C2 cannot be protonated by LYS175, both on thermodynamic and kinetic grounds. As the activation barrier of 35 kcal/mol calculated here (Figure ) for the LYS175 donor is significantly higher than the experimental activation free energy of 16 kcal/mol (corresponding to k cat ), , this conclusion is not likely to change if other computational methodologies , were adopted, quantum dynamic effects − included, or alternative DFT functional used (see also Figure S5 in the Supporting Information). This is in stark contrast to the Grotthuss mechanism, which predicts an activation energy in excellent agreement with the experiment (Figure ).…”