CHARMM: the biomolecular simulation program
BR Brooks, CL Brooks III… - Journal of …, 2009 - Wiley Online Library
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 …
QM/MM methods for biomolecular systems
HM Senn, W Thiel - Angewandte Chemie International Edition, 2009 - Wiley Online Library
Two are better than one: Quantum mechanics/molecular mechanics (QM/MM) methods are
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …
the state‐of‐the‐art computational technique for treating reactive and other “electronic” …
LAMMPS-a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
Since the classical molecular dynamics simulator LAMMPS was released as an open source
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
TA Halgren - Journal of computational chemistry, 1996 - Wiley Online Library
This article introduces MMFF94, the initial published version of the Merck molecular force
field (MMFF). It describes the objectives set for MMFF, the form it takes, and the range of …
field (MMFF). It describes the objectives set for MMFF, the form it takes, and the range of …
[BOOK][B] Essentials of computational chemistry: theories and models
CJ Cramer - 2013 - books.google.com
Essentials of Computational Chemistry provides a balanced introduction to this dynamic
subject. Suitable for both experimentalists and theorists, a wide range of samples and …
subject. Suitable for both experimentalists and theorists, a wide range of samples and …
A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
MW Mahoney, WL Jorgensen - The Journal of chemical physics, 2000 - pubs.aip.org
The ability of simple potential functions to reproduce accurately the density of liquid water
from− 37 to 100° C at 1 to 10 000 atm has been further explored. The result is the five-site …
from− 37 to 100° C at 1 to 10 000 atm has been further explored. The result is the five-site …
Force fields for protein simulations
Publisher Summary The chapter focuses on a general description of the force fields that are
most commonly used at present, and it gives an indication of the directions of current …
most commonly used at present, and it gives an indication of the directions of current …
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
A re-parameterization of the standard TIP4P water model for use with Ewald techniques is
introduced, providing an overall global improvement in water properties relative to several …
introduced, providing an overall global improvement in water properties relative to several …
Modeling and simulations of polymers: a roadmap
TE Gartner III, A Jayaraman - Macromolecules, 2019 - ACS Publications
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 …
Polarizable atomic multipole water model for molecular mechanics simulation
A new classical empirical potential is proposed for water. The model uses a polarizable
atomic multipole description of electrostatic interactions. Multipoles through the quadrupole …
atomic multipole description of electrostatic interactions. Multipoles through the quadrupole …