Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used
to provide a general scheme for chemical reactions in proteins. However, such approaches …

1. Introduction 2582. Set-up of MD simulations 2602.1 Constant-pressure dynamics 2602.2
Grand-canonical dynamics 2612.3 Boundary conditions 2613. Force fields 2623.1 Proteins …

DL_POLY is a general-purpose molecular dynamics simulation package, which was
developed by Daresbury Laboratory in the mid-1990s for the molecular simulation …

Reliable studies of enzymatic reactions by combined quantum mechanical/molecular
mechanics (QM/MM) approaches, with an ab initio description of the quantum region …

We recently described a method to compute accurate quantum mechanical free energies
[Rod, TH; Ryde, U. Phys. Rev. Lett. 2005, 94, 138302]. The method, which we term quantum …

Recent years have seen dramatic improvements in computer power, allowing ever more
challenging problems to be approached. In light of this, it is imperative to have a quantitative …

We present a molecular simulation protocol to compute free energies of binding, which
combines a QM/MM correction term with rigorous classical free energy techniques, thereby …

Neural networks can be used generate potential energy hypersurfaces by fitting to a data set
of energies at discrete geometries, as might be obtained from ab initio calculations. Prior …

A theoretical study of the structural and electronic properties of the chloride ion and water
molecules in the first hydration shell is presented. The calculations are performed on an …

The transformation of a pharmaceutical solid from an anhydrous crystal into a hydrated form
during drug development represents a risk to a product's safety and efficacy due to the …