The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials

Abstract

ABSTRACT:The Dynamo module library has been developed for the simulation of molecular systems using hybrid quantum mechanical (QM) and molecular mechanical (MM) potentials. Dynamo is not a program package but is a library of Fortran 90 modules that can be employed by those interested in writing their own programs for performing molecular simulations. The library supports a range of different types of molecular calculation including geometry optimizations, reaction-path determinations and molecular dynamics and Monte Carlo simulations. This article outlines the general structure and capabilities of the library and describes in detail Dynamo's semiempirical QM/MM hybrid potential. Results are presented to indicate three particular aspects of this implementation-the handling of long-range nonbonding interactions, the nature of the boundary between the quantum mechanical and molecular mechanical atoms and how to perform path-integral hybrid-potential molecular dynamics simulations.

Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package

“…34,35 The link atom approach is by far the simplest to implement, and if used carefully can give satisfactory results. 36 A recent study by König et al on the effect of different QM/MM frontier treatments with SCC-DFTB as the QM method also concluded that the effect of using different link atom schemes in QM/MM simulations is rather small, especially in reactions that conserve the total charge, and emphasizes that other technical details such as the treatment of long-range electrostatics can often play a more important role. 37 There are a number of ways to implement a link atom approach that deal with both the way the link atom is positioned, the way the forces on the link atom are propagated, and the way non-bonding interactions around the link atom are treated.…”

“…For DFTB calculations we use a link atom scheme developed as part of the re-writing of AMBER's semi-empirical QM/MM method is used. 26 This approach is similar to that used by Dynamo, 36 where the link atom is treated as part of the covalent bond between the QM and MM atoms bonded across the interface. Each time an energy or gradient calculation is to be done the link atom coordinates are automatically generated from the current coordinates of the QM and MM atoms making up the QM-MM covalent pair.…”

“…Such an approach is also advocated by other QM/MM software developers. 36 Once the QM gradient has been calculated the force on each link atom is re-distributed between the QM and MM link pair by application of the chain rule.…”

Reversibility and Diffusion in Mandelythiamin Decarboxylation. Searching Dynamical Effects in Decarboxylation Reactions

“…The quantum mechanics (QM) region consists of MTh (51 atoms) and was treated by the semiempirical method AM1 16 and the water molecules were described by means of the TIP3P potential 17 as implemented in fDynamo library. 18,19 Initially the system was optimized and equilibrated by means of conjugate gradient optimization and molecular dynamics (MD) simulations. A switched cutoff, from 12 to 14 Å, was employed for all non-bonded interactions.…”

“…All the quantum mechanics/molecular mechanics (QM/MM) calculations were carried out applying periodic boundary conditions using fDynamo library. 18,19 To analyze the energetics of the chemical reaction we performed the potential of mean force (PMF) at 298K. The distance C6-C7 (see Scheme 1) was employed as distinguished reaction coordinate.…”