相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。DFTB plus , a software package for efficient approximate density functional theory based atomistic simulations
B. Hourahine et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
The ONETEP linear-scaling density functional theory program
Joseph C. A. Prentice et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Array programming with NumPy
Charles R. Harris et al.
NATURE (2020)
Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
David J. Huggins et al.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2019)
Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett's Acceptance Ratio Methods
Timothy J. Giese et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Developing Consistent Molecular Dynamics Force Fields for Biological Chromophores via Force Matching
Kirsten Claridge et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2019)
Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials
David Dubbeldam et al.
ADVANCED THEORY AND SIMULATIONS (2019)
Perspective: Ab initio force field methods derived from quantum mechanics
Peng Xu et al.
JOURNAL OF CHEMICAL PHYSICS (2018)
Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching
Phillip S. Hudson et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale
Phillip S. Hudson et al.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2018)
PSI4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability
Robert M. Parrish et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15
Lee-Ping Wang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2017)
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Peter Eastman et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins
Edward Harder et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
Self-consistent implementation of meta-GGA functionals for the ONETEP linear-scaling electronic structure package
James C. Womack et al.
JOURNAL OF CHEMICAL PHYSICS (2016)
Benchmarking Density Functionals on Structural Parameters of Small-/Medium-Sized Organic Molecules
Eric Bremond et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)
The Cambridge Structural Database
Colin R. Groom et al.
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS (2016)
CHARMM additive and polarizable force fields for biophysics and computer-aided drug design
K. Vanommeslaeghe et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2015)
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
James A. Maier et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Robustness in the Fitting of Molecular Mechanics Parameters
Kenno Vanommeslaeghe et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)
Developing accurate molecular mechanics force fields for conjugated molecular systems
Hainam Do et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2015)
Paramfit: Automated Optimization of Force Field Parameters for Molecular Dynamics Simulations
Robin M. Betz et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)
Fitting of Dihedral Terms in Classical Force Fields as an Analytic Linear Least-Squares Problem
Chad W. Hopkins et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2014)
Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin
Manuel Doemer et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Efficient Parameterization of Torsional Terms for Force Fields
Steven K. Burger et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)
Building Force Fields: An Automatic, Systematic, and Reproducible Approach
Lee-Ping Wang et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)
Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data
Lee-Ping Wang et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data
Lei Huang et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Rapid Parameterization of Small Molecules Using the Force Field Toolkit
Christopher G. Mayne et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2013)
Nonlocal van der Waals density functional made simple and efficient
Riccardo Sabatini et al.
PHYSICAL REVIEW B (2013)
Biowaiver monograph for immediate-release solid oral dosage forms: Acetylsalicylic acid
Jennifer B. Dressman et al.
JOURNAL OF PHARMACEUTICAL SCIENCES (2012)
Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules
Pengyu Ren et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Performance of the van der Waals Density Functional VV10 and (hybrid)GGA Variants for Thermochemistry and Noncovalent Interactions
Waldemar Hujo et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
Marie Zgarbova et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Effect of the Damping Function in Dispersion Corrected Density Functional Theory
Stefan Grimme et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)
Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)
Lingle Wang et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2011)
Communication: Hybrid ensembles for improved force matching
Lee-Ping Wang et al.
JOURNAL OF CHEMICAL PHYSICS (2010)
Nonlocal van der Waals density functional: The simpler the better
Oleg A. Vydrov et al.
JOURNAL OF CHEMICAL PHYSICS (2010)
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
Stefan Grimme et al.
JOURNAL OF CHEMICAL PHYSICS (2010)
Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field
Devleena Shivakumar et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields
K. Vanommeslaeghe et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2010)
Current Status of the AMOEBA Polarizable Force Field
Jay W. Ponder et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Automated conformational energy fitting for force-field development
Olgun Guvench et al.
JOURNAL OF MOLECULAR MODELING (2008)
Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections
Jeng-Da Chai et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2008)
Well-tempered metadynamics: A smoothly converging and tunable free-energy method
Alessandro Barducci et al.
PHYSICAL REVIEW LETTERS (2008)
DFTB+, a sparse matrix-based implementation of the DFTB method
B. Aradi et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2007)
The SCC-DFTB method and its application to biological systems
M. Elstner
THEORETICAL CHEMISTRY ACCOUNTS (2006)
Introducing ONETEP: Linear-scaling density functional simulations on parallel computers
CK Skylaris et al.
JOURNAL OF CHEMICAL PHYSICS (2005)
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
S Patel et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Development and testing of a general amber force field
JM Wang et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
C Oostenbrink et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Escaping free-energy minima
A Laio et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
A stable fluctuating-charge polarizable model for molecular dynamics simulations: Application to aqueous electron transfers
K Ando
JOURNAL OF CHEMICAL PHYSICS (2001)
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
GA Kaminski et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2001)
Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment
M Elstner et al.
JOURNAL OF CHEMICAL PHYSICS (2001)
Energetics and structure of glycine and alanine based model peptides: Approximate SCC-DFTB, AM1 and PM3 methods in comparison with DFT, HF and MP2 calculations
M Elstner et al.
CHEMICAL PHYSICS (2001)