Machine learning implicit solvation for molecular dynamics

Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules

An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Poisson (FDP) model with the smooth permittivity method implemented in the OpenEye ZAP libraries. Explicit counter-ions, co-ions, and nucleic acid were treated with a Langevin dynamics molecular dynamics algorithm. Ion el...

Machine learning molecular dynamics for the simulation of infrared spectra.

Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio ...

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent-solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differe...

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics.

Dynamics of electron solvation in molecular clusters.

Solvated electrons, and hydrated electrons in particular, are important species in condensed phase chemistry, physics, and biology. Many studies have examined the formation mechanism, reactivity, spectroscopy, and dynamics of electrons in aqueous solution and other solvents, leading to a fundamental understanding of the electron-solvent interaction. However, key aspects of solvated electrons re...