| GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation | 2008/02/02 | English | 12,614 |
| ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB | 2015/07/23 | English | 6,442 |
| PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data | 2013/06/25 | English | 4,406 |
| Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions | 2006/02/04 | English | 3,199 |
| 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 | 2012/08/06 | English | 3,094 |
| NCIPLOT: A Program for Plotting Noncovalent Interaction Regions | 2011/01/25 | English | 2,837 |
| PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions | 2011/01/06 | English | 2,712 |
| MMPBSA.py: An Efficient Program for End-State Free Energy Calculations | 2012/08/16 | English | 2,653 |
| P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation | 2007/12/01 | English | 2,645 |
| Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald | 2013/08/20 | English | 2,247 |
| CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field | 2015/12/03 | English | 2,105 |
| OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins | 2015/12/01 | English | 2,089 |
| The MARTINI Coarse-Grained Force Field: Extension to Proteins | 2008/04/16 | English | 1,812 |
| GFN2-xTB—An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions | 2019/02/11 | English | 1,712 |
| Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born | 2012/04/15 | English | 1,420 |
| An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0 | 2011/11/15 | English | 1,324 |
| A Combined Charge and Energy Decomposition Scheme for Bond Analysis | 2009/03/02 | English | 1,323 |
| Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field | 2010/04/14 | English | 1,260 |
| Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values | 2011/06/09 | English | 1,250 |
| g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates | 2010/11/16 | English | 1,138 |
| Computational Thermochemistry: Scale Factor Databases and Scale Factors for Vibrational Frequencies Obtained from Electronic Model Chemistries | 2010/08/20 | English | 1,138 |
| Revised Basis Sets for the LANL Effective Core Potentials | 2008/06/07 | English | 1,112 |
| 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) | 2017/04/24 | English | 1,076 |
| All-Electron Scalar Relativistic Basis Sets for Third-Row Transition Metal Atoms | 2008/05/08 | English | 1,030 |
| Efficient and Accurate Double-Hybrid-Meta-GGA Density Functionals—Evaluation with the Extended GMTKN30 Database for General Main Group Thermochemistry, Kinetics, and Noncovalent Interactions | 2010/12/23 | English | 992 |
| Improved Parameters for the Martini Coarse-Grained Protein Force Field | 2012/11/28 | English | 962 |
| Benchmarking the Conductor-like Polarizable Continuum Model (CPCM) for Aqueous Solvation Free Energies of Neutral and Ionic Organic Molecules | 2004/11/13 | English | 939 |
| Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability | 2017/06/06 | English | 925 |
| Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions | 2008/10/15 | English | 917 |
| Performance of B3LYP Density Functional Methods for a Large Set of Organic Molecules | 2008/01/24 | English | 914 |