Force field evaluation for biomolecular simulation: free enthalpies of solvation of polar and apolar compounds in various solvents

scientific article published in March 2006

Force field evaluation for biomolecular simulation: free enthalpies of solvation of polar and apolar compounds in various solvents is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1002/CPHC.200500510
P698PubMed publication ID16514695

P50authorDaan P GeerkeQ40285012
Wilfred F van GunsterenQ52153822
P2860cites workAn Effective Force Field for Molecular Dynamics Simulations of Dimethyl Sulfoxide and Dimethyl Sulfoxide−Water MixturesQ63915597
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic LiquidsQ99192955
All-atom empirical potential for molecular modeling and dynamics studies of proteinsQ27860468
Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solutionQ29014511
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanesQ29397708
The missing term in effective pair potentialsQ29542481
A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6Q29617517
Free energy via molecular simulation: applications to chemical and biomolecular systemsQ38648060
Calculation of the free energy of solvation for neutral analogs of amino acid side chainsQ43956197
Calculation of the water–cyclohexane transfer free energies of neutral amino acid side‐chain analogs using the OPLS all‐atom force fieldQ44600334
A general treatment of solubility. 1. The QSPR correlation of solvation free energies of single solutes in series of solventsQ44665073
Modeling nonionic aqueous solutions: the acetone-water mixtureQ45212904
A new GROMOS force field for hexopyranose-based carbohydratesQ46611601
Amine hydration: a united-atom force-field solutionQ46630960
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambinQ47682341
Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.Q51633889
CHARMM: A program for macromolecular energy, minimization, and dynamics calculationsQ53340989
AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactionsQ53341450
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic MoleculesQ55918670
An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phaseQ56225272
An improved nucleic acid parameter set for the GROMOS force fieldQ56225273
Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteinsQ56776034
Predicting aqueous solubilities from aqueous free energies of solvation and experimental or calculated vapor pressures of pure substancesQ57250591
Accounting for polarization in molecular simulationQ57269352
Molecular dynamics with coupling to an external bathQ57569060
The GROMOS Biomolecular Simulation Program PackageQ57746723
Affinities of amino acid side chains for solvent waterQ57948314
A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force fieldQ58005581
Derivation of an improved simple point charge model for liquid water: SPC/A and SPC/LQ58616227
Parametrization of aliphatic CHn united atoms of GROMOS96 force fieldQ58616298
P433issue3
P921main subjectenthalpyQ161064
force fieldQ1341441
P304page(s)671-678
P577publication date2006-03-01
P1433published inChemPhysChemQ2012739
P1476titleForce field evaluation for biomolecular simulation: free enthalpies of solvation of polar and apolar compounds in various solvents
P478volume7

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cites work (P2860)
Q37826630Accounting for electronic polarization in non-polarizable force fields
Q30494073Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field
Q46862721Chemical potential of liquids and mixtures via adaptive resolution simulation
Q41906611Electronic continuum model for molecular dynamics simulations
Q42967065Electronic continuum model for molecular dynamics simulations of biological molecules
Q34154833How sequence determines elasticity of disordered proteins
Q41904845Polarizable Mean-Field Model of Water for Biological Simulations with Amber and Charmm force fields
Q58048746Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field
Q58048721Prediction of hydration free energies for the SAMPL4 diverse set of compounds using molecular dynamics simulations with the OPLS-AA force field
Q57634715Prediction of then-hexane/water and 1-octanol/water partition coefficients for environmentally relevant compounds using molecular simulation
Q41466309Structural properties of methanol-water binary mixtures within the quantum cluster equilibrium model.
Q34000276Transient hydrogen bonding in uniformly ¹³C,¹⁵N-labeled carbohydrates in water.
Q37095169Using MD Simulations To Calculate How Solvents Modulate Solubility
Q44668468Using molecular simulation to predict solute solvation and partition coefficients in solvents of different polarity

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