Affordable Ab Initio Path Integral for Thermodynamic Properties via Molecular Dynamics Simulations Using Semiempirical Reference Potential
出版年份 2021 全文链接
标题
Affordable Ab Initio Path Integral for Thermodynamic Properties via Molecular Dynamics Simulations Using Semiempirical Reference Potential
作者
关键词
-
出版物
JOURNAL OF PHYSICAL CHEMISTRY A
Volume 125, Issue 50, Pages 10677-10685
出版商
American Chemical Society (ACS)
发表日期
2021-12-13
DOI
10.1021/acs.jpca.1c07727
参考文献
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。- Biomolecular QM/MM Simulations: What Are Some of the “Burning Issues”?
- (2021) Qiang Cui et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 4. Adaptive QM/MM
- (2021) Jia-Ning Wang et al. Journal of Chemical Theory and Computation
- Machine Learning in QM/MM Molecular Dynamics Simulations of Condensed-Phase Systems
- (2021) Lennard Böselt et al. Journal of Chemical Theory and Computation
- Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions
- (2021) Xiaoliang Pan et al. Journal of Chemical Theory and Computation
- Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution
- (2021) Jinzhe Zeng et al. Journal of Chemical Theory and Computation
- Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability
- (2021) Bryant Kim et al. Journal of Chemical Theory and Computation
- Free energy level correction by Monte Carlo resampling with weighted histogram analysis method
- (2020) Seyoung Chung et al. CHINESE JOURNAL OF CHEMICAL PHYSICS
- Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 3. Gaussian Smoothing on Density-of-States
- (2020) Wenxin Hu et al. Journal of Chemical Theory and Computation
- Enhanced Sampling Path Integral Methods Using Neural Network Potential Energy Surfaces with Application to Diffusion in Hydrogen Hydrates
- (2020) Joseph R. Cendagorta et al. Advanced Theory and Simulations
- Impact of nuclear quantum effects on the structural inhomogeneity of liquid water
- (2019) Arian Berger et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- On the use of interaction energies in QM/MM free energy simulations
- (2019) Phillip S. Hudson et al. Journal of Chemical Theory and Computation
- Accurate Quantum Chemical Free Energies at Affordable Cost
- (2019) GiovanniMaria Piccini et al. Journal of Physical Chemistry Letters
- SCC-DFTB-PIMD Method To Evaluate a Multidimensional Quantum Free-Energy Surface for a Proton-Transfer Reaction
- (2019) Kento Kosugi et al. Journal of Chemical Theory and Computation
- Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett’s Acceptance Ratio Methods
- (2019) Timothy J. Giese et al. Journal of Chemical Theory and Computation
- Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks
- (2018) Lin Shen et al. Journal of Chemical Theory and Computation
- On the convergence of multi-scale free energy simulations
- (2018) Gerhard König et al. MOLECULAR SIMULATION
- Nuclear quantum effects enter the mainstream
- (2018) Thomas E. Markland et al. Nature Reviews Chemistry
- Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching
- (2018) Phillip S. Hudson et al. Journal of Chemical Theory and Computation
- Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation
- (2018) Pengfei Li et al. Journal of Chemical Theory and Computation
- Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations
- (2017) Jingheng Wu et al. JOURNAL OF CHEMICAL PHYSICS
- A unified thermostat scheme for efficient configurational sampling for classical/quantum canonical ensembles via molecular dynamics
- (2017) Zhijun Zhang et al. JOURNAL OF CHEMICAL PHYSICS
- Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities
- (2017) Fiona L. Kearns et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges
- (2016) Michele Ceriotti et al. CHEMICAL REVIEWS
- A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat
- (2016) Jian Liu et al. JOURNAL OF CHEMICAL PHYSICS
- Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods
- (2016) V. Kapil et al. JOURNAL OF CHEMICAL PHYSICS
- Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory
- (2016) Ondrej Marsalek et al. JOURNAL OF CHEMICAL PHYSICS
- Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials
- (2016) Eric C. Dybeck et al. Journal of Chemical Theory and Computation
- Accelerating Ab Initio Path Integral Simulations via Imaginary Multiple-Timestepping
- (2016) Xiaolu Cheng et al. Journal of Chemical Theory and Computation
- Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks
- (2016) Lin Shen et al. Journal of Chemical Theory and Computation
- Convergence of single-step free energy perturbation
- (2016) Stefan Boresch et al. MOLECULAR PHYSICS
- Recent advances in QM/MM free energy calculations using reference potentials
- (2015) Fernanda Duarte et al. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
- Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes
- (2015) Phillip S. Hudson et al. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
- The ONIOM Method and Its Applications
- (2015) Lung Wa Chung et al. CHEMICAL REVIEWS
- Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States
- (2015) Elizabeth Brunk et al. CHEMICAL REVIEWS
- Path Integral Metadynamics
- (2015) Ruge Quhe et al. Journal of Chemical Theory and Computation
- 15N and 1H Solid-State NMR Investigation of a Canonical Low-Barrier Hydrogen-Bond Compound: 1,8-Bis(dimethylamino)naphthalene
- (2015) Paul B. White et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems
- (2015) Phillip S. Hudson et al. Journal of Physical Chemistry Letters
- Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes
- (2014) Gerhard König et al. Journal of Chemical Theory and Computation
- Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations
- (2014) Yan Zhou et al. Journal of Chemical Theory and Computation
- Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation
- (2013) Iakov Polyak et al. JOURNAL OF CHEMICAL PHYSICS
- Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations
- (2012) Jimmy Heimdal et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- A Simple QM/MM Approach for Capturing Polarization Effects in Protein−Ligand Binding Free Energy Calculations
- (2011) Frank R. Beierlein et al. JOURNAL OF PHYSICAL CHEMISTRY B
- The inefficiency of re-weighted sampling and the curse of system size in high-order path integration
- (2011) M. Ceriotti et al. PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
- Aqueous Basic Solutions: Hydroxide Solvation, Structural Diffusion, and Comparison to the Hydrated Proton
- (2010) Dominik Marx et al. CHEMICAL REVIEWS
- Efficient stochastic thermostatting of path integral molecular dynamics
- (2010) Michele Ceriotti et al. JOURNAL OF CHEMICAL PHYSICS
- A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
- (2010) Stefan Grimme et al. JOURNAL OF CHEMICAL PHYSICS
- Non-Boltzmann sampling and Bennett's acceptance ratio method: How to profit from bending the rules
- (2010) Gerhard König et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- QM/MM Methods for Biomolecular Systems
- (2009) Hans Martin Senn et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods
- (2008) Hao Hu et al. Annual Review of Physical Chemistry
- A refined ring polymer contraction scheme for systems with electrostatic interactions
- (2008) Thomas E. Markland et al. CHEMICAL PHYSICS LETTERS
- Combining quantum wavepacket ab initio molecular dynamics with QM/MM and QM/QM techniques: Implementation blending ONIOM and empirical valence bond theory
- (2008) Isaiah Sumner et al. JOURNAL OF CHEMICAL PHYSICS
- Adaptively biased molecular dynamics for free energy calculations
- (2008) Volodymyr Babin et al. JOURNAL OF CHEMICAL PHYSICS
- Statistically optimal analysis of samples from multiple equilibrium states
- (2008) Michael R. Shirts et al. JOURNAL OF CHEMICAL PHYSICS
- An efficient ring polymer contraction scheme for imaginary time path integral simulations
- (2008) Thomas E. Markland et al. JOURNAL OF CHEMICAL PHYSICS
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now