Pair Interaction Energy Decomposition Analysis for Density Functional Theory and Density-Functional Tight-Binding with an Evaluation of Energy Fluctuations in Molecular Dynamics

Abstract

Pair interaction energy decomposition analysis in the fragment molecular orbital (FMO) method is extended to treat density functional theory (DFT) and density-functional tight-binding (DFTB). Fluctuations of energy contributions are obtained from molecular dynamics simulations. Interactions at the DFT and DFTB levels are compared to the values obtained with Hartree-Fock, second-order Møller-Plesset (MP2), and coupled cluster methods. Hydrogen bonding in water clusters is analyzed. 200 ps NVT molecular dynamics simulations are performed with FMO for two ligands bound to the Trp-cage miniprotein (PDB 1L2Y ); the fluctuations of fragment energies and interactions are analyzed.

Empirical corrections and pair interaction energies in the fragment molecular orbital method

“…. For density-functional tight-binding (DFTB) [36,28] PIEDA has different components: It is important to understand the difference between interaction and binding energies. Interaction energies IJ E D in FMO are pairwise binding energies between electrostatically interacting polarized fragments, whereas the binding energy E D for a cluster is the amount of energy gained by forming the complex from isolated non-interacting fragments.…”

“…The timings T (min) are for a dual 12-core 2.2 GHz Xeon node (12 cores total). 7.5 11.9 a DFTB3-D3(BJ)/3ob results are taken from [28]. Using AB (cc-pVDZ:aug-cc-pVDZ) for MP2.…”

Exploring the Mechanism of Olfactory Recognition at the Initial Stage by Modeling the Emission Spectrum of Electron Transfer

“…From the point of view of molecular interaction, if the two molecules are close enough to interact with each other, there is a charge transfer energy component in the total intermolecular interaction energy [79][80][81]. By the energy decomposition analysis (EDA), the intermolecular interaction energy can be partitioned into energy components such as electrostatic, polarization, charge transfer, exchange and correlation contributions and related chemical henomena [82];…”

Multithreaded parallelization of the energy and analytic gradient in the fragment molecular orbital method

“…The accuracy can be systematically improved by increasing the order of the many‐body expansion . FMO has been used to analyze protein‐ligand binding, model chemical reactions in enzymes, optimize protein structures, build coarse grained models for molecular dynamics (MD), obtain density of states (DOS) of materials and study electron excitations …”

“…[29] The accuracy can be systematically improved by increasing the order of the many-body expansion. [30] FMO has been used to analyze protein-ligand binding, [31][32][33][34] model chemical reactions in enzymes, [35] optimize protein structures, [36] build coarse grained models for molecular dynamics (MD), [37] obtain density of states (DOS) of materials [38] and study electron excitations. [39] FMO method has been parallelized with high efficiency, [40,41] in GAMESS, [42,43] using generalized distributed data interface (GDDI), [44,45] and in other programs: ABINIT-MP, [46] OpenFMO, [47] and PAICS, [48] ABINIT-MP has been efficiently parallelized on the Earth Simulator [49] and K [34] supercomputers.…”