Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

Abstract

The ultrafast nuclear dynamics of the acetylene cation C 2 H 2 + following photoionization of the neutral molecule is investigated using an extreme-ultraviolet pump/infrared probe setup. The observed modulation of the C 2 H + fragment ion yield with pump-probe delay is related to structural changes induced by the extreme-ultraviolet pump pulse taking place on the femtosecond timescale. High-level simulations suggest that the trans-bending and CC bond stretching motion of the C 2 H 2 + cation govern the observed interaction with the infrared pulse. Depending on the molecular configuration at arrival of the infrared pulse, it either transfers population to higher-lying states or to the C 2 H 2 + ground state, thereby enhancing or lowering the C 2 H + yield. Our ultrafast pump-probe scheme can thus be used to track excited state nuclear dynamics with a resolution of a few femtoseconds, leading the way to studying fast dynamics also in larger hydrocarbon molecules.

MiMiC: Multiscale Modeling in Computational Chemistry

“…Benchmarks were performed using Troullier-Martins pseudopotentials (Troullier and Martins, 1991). The average wall time of a single MD time step is around 13 s (Bolnykh et al, 2019) when computationally demanding hybrid exchange-correlation functionals, such as B3LYP (Becke, 1988(Becke, , 1993Lee et al, 1988), are employed. This enables nanosecondscale QM/MM MD simulations to be performed, which in turn allows one to obtain converged free energy calculations of biological systems if enough computational resources are available.…”

“…However, with the field rapidly growing, new simulation paradigms and approaches might quickly emerge, clearly favoring strategy (2) over (1). In the following, we show that flexibility does not necessarily come at the expense of a high computation (or communication) overhead by presenting the recently developed MiMiC framework (Bolnykh et al, 2019;Olsen et al, 2019) that combines the capability of performing fast and efficient multiscale molecular dynamics (MD) simulations with facile support for flexible extensions. These objectives are achieved by applying (2) with an efficient method to exchange data among the coupled software packages.…”

Expanding the boundaries of ligand–target modeling by exascale calculations

“…[90][91][92][93] A hybrid QM/MM interface. The Multiscale Modeling in Chemistry (or MiMiC) 51,94 interface joins GROMACS with the CPMD code. 95 The latter implements DFT-based MD with high levels of parallel performance using plane-wave (PW) basis sets.…”

“…50 Furthermore, although generally of much higher computational cost, QM/MM codes may scale better than force field-based MD with the number of processors. 51 Prompted by the importance of HPC for modern computational biochemistry and pharmacology, we have here compiled a review focusing on technical aspects of high-performance computing (HPC) aspects particularly relevant for MD and molecular docking. Obviously, because we deal mostly with methods rather than applications, the material can be useful also for readers interested in the use of these techniques for applications other than those dealt with here.…”

On the accuracy of molecular simulation-based predictions of koffvalues: a Metadynamics study

“…To make these computationally feasible we use a QM/MM approach as implemented in the MiMiC multiscale interface. 32,33 The QM part of the system consists of the ligand and its interacting groups (Fig. 5a-c, See Methods for details).…”