(Q33784252)

29 July 2017

title

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems (English)

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29 July 2017

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1

William L Jorgensen

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29 July 2017

2

Julian Tirado-Rives

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29 July 2017

language of work or name

English

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publication date

3 May 2005

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Proceedings of the National Academy of Sciences of the United States of America

29 July 2017

published in

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29 July 2017

volume

102

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29 July 2017

issue

19

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29 July 2017

page(s)

6665-6670

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

29 July 2017

cites work

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Optimization of Effective Atom Centered Potentials for London Dispersion Forces in Density Functional Theory

4 July 2018

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Melting points and thermal expansivities of proton-disordered hexagonal ice with several model potentials

4 July 2018

1 reference

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Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

4 July 2018

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A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums

4 July 2018

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A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

4 July 2018

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Empirical force fields for biological macromolecules: overview and issues.

4 July 2018

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CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.

4 July 2018

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Development and testing of a general amber force field

4 July 2018

1 reference

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Force fields for protein simulations

4 July 2018

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Modeling biotransformation reactions by combined quantum mechanical/molecular mechanical approaches: from structure to activity

4 July 2018

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Computer simulations of enzyme catalysis: methods, progress, and insights

4 July 2018

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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation

4 July 2018

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The role and perspective of ab initio molecular dynamics in the study of biological systems

4 July 2018

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Improved simulation of liquid water by molecular dynamics

4 July 2018

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Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94

21 January 2018

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Ion solvation thermodynamics from simulation with a polarizable force field

21 January 2018

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Cation-pi interactions: an energy decomposition analysis and its implication in delta-opioid receptor-ligand binding

21 January 2018

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Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

21 January 2018

1 reference

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Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408037102

Improved treatment of the protein backbone in empirical force fields.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408037102

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408037102

Accuracy of free energies of hydration using CM1 and CM3 atomic charges

21 January 2018

1 reference

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Class IV charge models: A new semiempirical approach in quantum chemistry

21 January 2018

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Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYP

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408037102

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408037102

A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408037102

Water structure from scattering experiments and simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408037102

Temperature and size dependence for Monte Carlo simulations of TIP4P water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408037102

Towards an assessment of the accuracy of density functional theory for first principles simulations of water

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408037102

A simple polarizable model of water based on classical Drude oscillators

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408037102

Molecular dynamics simulation of the ice nucleation and growth process leading to water freezing

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0408037102

Interplay between Time-Temperature Transformation and the Liquid-Liquid Phase Transition in Water

21 January 2018

1 reference

12 December 2020

Hydrogen bonding in water

1 reference

12 December 2020

Phase diagram of water from computer simulation

1 reference

12 December 2020

Tracing the phase diagram of the four-site water potential (TIP4P)

1 reference

12 December 2020

Temperature dependence of the hydrophobic hydration and interaction of simple solutes: an examination of five popular water models

1 reference

12 December 2020

Excess free energy of liquids from molecular dynamics simulations. Application to water models

1 reference

12 December 2020

Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator

1 reference

12 December 2020

Efficient Simulation Method for Polarizable Protein Force Fields: Application to the Simulation of BPTI in Liquid Water.

1 reference

12 December 2020

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

1 reference

12 December 2020

Spinodal of liquid water

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0408037102

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29 July 2017

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29 July 2017

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