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 …
Empirical force fields for biological macromolecules: overview and issues
AD MacKerell Jr - Journal of computational chemistry, 2004 - Wiley Online Library
Empirical force field‐based studies of biological macromolecules are becoming a common
tool for investigating their structure–activity relationships at an atomic level of detail. Such …
tool for investigating their structure–activity relationships at an atomic level of detail. Such …
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the …
We describe the development, current features, and some directions for future development
of the AMBER package of computer programs. This package has evolved from a program …
of the AMBER package of computer programs. This package has evolved from a program …
[BOOK][B] The theory of intermolecular forces
A Stone - 2013 - books.google.com
The theory of intermolecular forces has advanced very greatly in recent years. It has become
possible to carry out accurate calculations of intermolecular forces for molecules of useful …
possible to carry out accurate calculations of intermolecular forces for molecules of useful …
A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
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 …
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 …
Dynamical fluctuating charge force fields: Application to liquid water
A new molecular dynamics model in which the point charges on atomic sites are allowed to
fluctuate in response to the environment is developed and applied to water. The idea for …
fluctuate in response to the environment is developed and applied to water. The idea for …
QM/MM: what have we learned, where are we, and where do we go from here?
This paper briefly reviews the current status of the most popular methods for combined
quantum mechanical/molecular mechanical (QM/MM) calculations, including their …
quantum mechanical/molecular mechanical (QM/MM) calculations, including their …
How water's properties are encoded in its molecular structure and energies
How are water's material properties encoded within the structure of the water molecule? This
is pertinent to understanding Earth's living systems, its materials, its geochemistry and …
is pertinent to understanding Earth's living systems, its materials, its geochemistry and …
Polarizable atomic multipole-based AMOEBA force field for proteins
Development of the AMOEBA (atomic multipole optimized energetics for biomolecular
simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes …
simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes …