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GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features
Progress is reported in graphics processing unit (GPU)-accelerated molecular dynamics and free energy methods in Amber, including free energy perturbation and thermodynamic integration methods with support for nonlinear soft-core potential and parameter interpolation transformation pathways. Expand
Density-functional expansion methods: evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations.
The results suggest that the origin of the short-range repulsive potential within self-consistent charge density-functional tight-binding methods mainly arises from the approximations made to the first-order matrix elements. Expand
Complete basis set extrapolated potential energy, dipole, and polarizability surfaces of alkali halide ion-neutral weakly avoided crossings with and without applied electric fields.
Complete basis set extrapolations of alkali halide energy, dipole, and polarizability surfaces are performed with and without applied fields along the internuclear axis using state-averaged multireference configuration interaction to provide benchmark data for the development of new-generation many-body force fields that are able to model charge transfer. Expand
Development of a Robust Indirect Approach for MM→QM Free Energy Calculations that Combines Force-matched Reference Potential and Bennett's Acceptance Ratio Methods.
It is found that Zwanzig's equation is inadequate unless a large number of intermediate states are explicitly simulated, and computational resources may be used more efficiently by running multiple simulations for no more than 50 ps, rather than running one long simulation. Expand
Multipolar Ewald Methods, 1: Theory, Accuracy, and Performance
The Ewald, Particle Mesh Ewald (PME), and Fast Fourier–Poisson (FFP) methods are developed for systems composed of spherical multipole moment expansions. A unified set of equations is derived thatExpand
Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations.
A new model for nonelectrostatic nonbonded interactions in QMMM calculations that overcomes many of these problems is proposed, based on a scaled overlap model for repulsive exchange and attractive dispersion interactions that is a function of atomic charge. Expand
Many-body force field models based solely on pairwise Coulomb screening do not simultaneously reproduce correct gas-phase and condensed-phase polarizability limits.
It is demonstrated that many-body force field models based solely on pairwise Coulomb screening cannot simultaneously reproduce both gas-phase and condensed-phase polarizability limits, and that coupling with non-classical many- body effects, in particular exchange terms, may be important. Expand
Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods
This work provides benchmark abinitio gas-phase two-dimensional potential energy scans of the RNA and DNA sugar puckering and demonstrates that the uncorrected semiempirical models do not usually produce a transition state between the A-form and B-form sugar puckers, but the ab initio transition state is reproduced when the B-spline correction is used. Expand
Evidence for the Role of Active Site Residues in the Hairpin Ribozyme from Molecular Simulations along the Reaction Path
The structure and dynamics of key active site residues are explored using more than 1 μs of molecular dynamics simulations of the hairpin ribozyme at different stages along the catalytic pathway to suggest a possible alternative role for G8 to promote inline fitness and facilitate activation of the nucleophile by hydrogen bonding. Expand