CHARMM: the biomolecular simulation program
Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …
widely used molecular simulation program. It has been developed over the last three …
Advances in methods and algorithms in a modern quantum chemistry program package
Advances in theory and algorithms for electronic structure calculations must be incorporated
into program packages to enable them to become routinely used by the broader chemical …
into program packages to enable them to become routinely used by the broader chemical …
TeraChem: A graphical processing unit‐accelerated electronic structure package for large‐scale ab initio molecular dynamics
TeraChem was born in 2008 with the goal of providing fast on‐the‐fly electronic structure
calculations to facilitate ab initio molecular dynamics studies of large biochemical systems …
calculations to facilitate ab initio molecular dynamics studies of large biochemical systems …
Modeling and simulations of polymers: a roadmap
Molecular modeling and simulations are invaluable tools for the polymer science and
engineering community. These computational approaches enable predictions and provide …
engineering community. These computational approaches enable predictions and provide …
Optimization methods for finding minimum energy paths
A comparison of chain-of-states based methods for finding minimum energy pathways
(MEPs) is presented. In each method, a set of images along an initial pathway between two …
(MEPs) is presented. In each method, a set of images along an initial pathway between two …
Using collective variables to drive molecular dynamics simulations
A software framework is introduced that facilitates the application of biasing algorithms to
collective variables of the type commonly employed to drive massively parallel molecular …
collective variables of the type commonly employed to drive massively parallel molecular …
Efficient methods for finding transition states in chemical reactions: Comparison of improved dimer method and partitioned rational function optimization method
A combination of interpolation methods and local saddle-point search algorithms is probably
the most efficient way of finding transition states in chemical reactions. Interpolation methods …
the most efficient way of finding transition states in chemical reactions. Interpolation methods …
Systematic exploration of the mechanism of chemical reactions: the global reaction route map** (GRRM) strategy using the ADDF and AFIR methods
S Maeda, K Ohno, K Morokuma - Physical Chemistry Chemical Physics, 2013 - pubs.rsc.org
Global reaction route map** (GRRM), a fully-automated search for all important reaction
pathways relevant to a given purpose, on the basis of quantum chemical calculations …
pathways relevant to a given purpose, on the basis of quantum chemical calculations …
Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems
Machine learning encompasses tools and algorithms that are now becoming popular in
almost all scientific and technological fields. This is true for molecular dynamics as well …
almost all scientific and technological fields. This is true for molecular dynamics as well …
Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration
We review a selection of methods for performing enhanced sampling in molecular dynamics
simulations. We consider methods based on collective variable biasing and on tempering …
simulations. We consider methods based on collective variable biasing and on tempering …