Motivation The generation of parameter files for molecular dynamics (MD) simulations of
small molecules that are suitable for force fields commonly applied to proteins and nucleic …

Molecular dynamics (MD) simulation engines use a variety of different approaches for
modeling molecular systems with force fields that govern their dynamics and describe their …

Molecular dynamics simulations are being applied to increasingly complex systems,
including those involving small endogenous compounds and drug molecules. In order to …

Amber is the collective name for a suite of programs that allow users to carry out molecular
dynamics simulations, particularly on biomolecules. None of the individual programs carries …

We describe a complete implementation of Martini 2 and Martini 3 in the OpenMM molecular
dynamics software package. Martini is a widely used coarse-grained force field with …

The ensemble of structures generated by molecular mechanics (MM) simulations is
determined by the functional form of the force field employed and its parameterization. For a …

Molecular dynamics (MD) simulations have become increasingly popular in studying the
motions and functions of biomolecules. The accuracy of the simulation, however, is highly …

The Automated force field Topology Builder (ATB, http://compbio. biosci. uq. edu. au/atb) is a
Web-accessible server that can provide topologies and parameters for a wide range of …

Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological
processes. Accurate MD simulations require computationally demanding quantum …

Molecular dynamics (MD) simulations allow insights into complex processes, but accurate
MD simulations require costly quantum-mechanical calculations. For larger systems, efficient …