# | Title | Journal | Year | Citations |
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1 | GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation | Journal of Chemical Theory and Computation | 2008 | 13,875 |
2 | ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB | Journal of Chemical Theory and Computation | 2015 | 7,322 |
3 | PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data | Journal of Chemical Theory and Computation | 2013 | 4,960 |
4 | Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles | Journal of Chemical Theory and Computation | 2012 | 3,696 |
5 | Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions | Journal of Chemical Theory and Computation | 2006 | 3,329 |
6 | PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions | Journal of Chemical Theory and Computation | 2011 | 3,121 |
7 | P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation | Journal of Chemical Theory and Computation | 2008 | 2,976 |
8 | NCIPLOT: A Program for Plotting Noncovalent Interaction Regions | Journal of Chemical Theory and Computation | 2011 | 2,897 |
9 | MMPBSA.py: An Efficient Program for End-State Free Energy Calculations | Journal of Chemical Theory and Computation | 2012 | 2,891 |
10 | Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald | Journal of Chemical Theory and Computation | 2013 | 2,598 |
11 | CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field | Journal of Chemical Theory and Computation | 2016 | 2,567 |
12 | OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins | Journal of Chemical Theory and Computation | 2016 | 2,349 |
13 | The MARTINI Coarse-Grained Force Field: Extension to Proteins | Journal of Chemical Theory and Computation | 2008 | 2,178 |
14 | GFN2-xTB—An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions | Journal of Chemical Theory and Computation | 2019 | 1,704 |
15 | Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born | Journal of Chemical Theory and Computation | 2012 | 1,633 |
16 | Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values | Journal of Chemical Theory and Computation | 2011 | 1,436 |
17 | An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0 | Journal of Chemical Theory and Computation | 2011 | 1,425 |
18 | Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field | Journal of Chemical Theory and Computation | 2010 | 1,360 |
19 | A Combined Charge and Energy Decomposition Scheme for Bond Analysis | Journal of Chemical Theory and Computation | 2009 | 1,350 |
20 | g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates | Journal of Chemical Theory and Computation | 2010 | 1,284 |
21 | Computational Thermochemistry: Scale Factor Databases and Scale Factors for Vibrational Frequencies Obtained from Electronic Model Chemistries | Journal of Chemical Theory and Computation | 2010 | 1,183 |
22 | Improved Parameters for the Martini Coarse-Grained Protein Force Field | Journal of Chemical Theory and Computation | 2013 | 1,181 |
23 | Revised Basis Sets for the LANL Effective Core Potentials | Journal of Chemical Theory and Computation | 2008 | 1,162 |
24 | A Robust and Accurate Tight-Binding Quantum Chemical Method for Structures, Vibrational Frequencies, and Noncovalent Interactions of Large Molecular Systems Parametrized for All spd-Block Elements (Z = 1–86) | Journal of Chemical Theory and Computation | 2017 | 1,072 |
25 | Lipid14: The Amber Lipid Force Field | Journal of Chemical Theory and Computation | 2014 | 1,068 |
26 | All-Electron Scalar Relativistic Basis Sets for Third-Row Transition Metal Atoms | Journal of Chemical Theory and Computation | 2008 | 1,061 |
27 | Efficient and Accurate Double-Hybrid-Meta-GGA Density Functionals—Evaluation with the Extended GMTKN30 Database for General Main Group Thermochemistry, Kinetics, and Noncovalent Interactions | Journal of Chemical Theory and Computation | 2011 | 1,035 |
28 | The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design | Journal of Chemical Theory and Computation | 2017 | 1,032 |
29 | Benchmarking the Conductor-like Polarizable Continuum Model (CPCM) for Aqueous Solvation Free Energies of Neutral and Ionic Organic Molecules | Journal of Chemical Theory and Computation | 2005 | 977 |
30 | Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability | Journal of Chemical Theory and Computation | 2017 | 961 |
31 | Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions | Journal of Chemical Theory and Computation | 2008 | 956 |
32 | Extensive TD-DFT Benchmark: Singlet-Excited States of Organic Molecules | Journal of Chemical Theory and Computation | 2009 | 942 |
33 | Performance of B3LYP Density Functional Methods for a Large Set of Organic Molecules | Journal of Chemical Theory and Computation | 2008 | 931 |
34 | Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning | Journal of Chemical Theory and Computation | 2015 | 896 |
35 | PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models | Journal of Chemical Theory and Computation | 2015 | 876 |
36 | Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles | Journal of Chemical Theory and Computation | 2011 | 873 |
37 | Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models | Journal of Chemical Theory and Computation | 2010 | 866 |
38 | A Qualitative Index of Spatial Extent in Charge-Transfer Excitations | Journal of Chemical Theory and Computation | 2011 | 858 |
39 | Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM | Journal of Chemical Theory and Computation | 2006 | 855 |
40 | Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations | Journal of Chemical Theory and Computation | 2015 | 847 |
41 | ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution | Journal of Chemical Theory and Computation | 2020 | 843 |
42 | Benchmark Databases for Nonbonded Interactions and Their Use To Test Density Functional Theory | Journal of Chemical Theory and Computation | 2005 | 832 |
43 | DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB) | Journal of Chemical Theory and Computation | 2011 | 828 |
44 | S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures | Journal of Chemical Theory and Computation | 2011 | 821 |
45 | Using Hessian Updating To Increase the Efficiency of a Hessian Based Predictor-Corrector Reaction Path Following Method | Journal of Chemical Theory and Computation | 2005 | 810 |
46 | ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale | Journal of Chemical Theory and Computation | 2009 | 771 |
47 | TD-DFT Performance for the Visible Absorption Spectra of Organic Dyes: Conventional versus Long-Range Hybrids | Journal of Chemical Theory and Computation | 2008 | 766 |
48 | Excitation Gaps of Finite-Sized Systems from Optimally Tuned Range-Separated Hybrid Functionals | Journal of Chemical Theory and Computation | 2012 | 765 |
49 | Parametrization and Benchmark of DFTB3 for Organic Molecules | Journal of Chemical Theory and Computation | 2013 | 743 |
50 | Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics | Journal of Chemical Theory and Computation | 2009 | 734 |