Comparison of software for molecular mechanics modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
| Name | View 3D | Model builder | Min | MD | MC | REM | QM | Imp | GPU | Comments | License | Website |
| AMBER | High Performance MD, Comprehensive analysis tools | , | ||||||||||
| Abalone | Biomolecular simulations, protein folding. | , gratis, commercial | ||||||||||
| ADF | Modeling suite: ReaxFF, UFF, QM-MM with Amber and Tripos force fields, DFT and semi-empirical methods, conformational analysis with RDKit; partly GPU-accelerated | , commercial, gratis trial | ||||||||||
| Ascalaph Designer | Molecular building, molecular dynamics, GPU acceleration | |||||||||||
| Avogadro | Molecule building, editing, conformational analysis, 2D/3D conversion; extensible interfaces to other tools | open source GNU GPL | ||||||||||
| BOSS | OPLS | |||||||||||
| CHARMM | Commercial version with multiple graphical front ends is sold by BIOVIA, formerly Accelrys. | , commercial | ||||||||||
| CHEMKIN | Chemical reaction kinetics. | |||||||||||
| CP2K | CP2K can perform atomistic and molecular simulations of solid state, liquid and biological systems. | open source GNU GPLv2 or later | ||||||||||
| Desmond | High performance MD; has comprehensive GUI to build, visualize, and review results and calculation setup up and launch | , commercial or gratis | ||||||||||
| Discovery Studio | Comprehensive life science modeling and simulation suite of applications focused on optimizing drug discovery process: small molecule simulations, QM-MM, pharmacophore modeling, QSAR, protein-ligand docking, protein homology modeling, sequence analysis, protein-protein docking, antibody modeling, etc. | , trial available | ||||||||||
| fold.it | Y / I | University of Washington and The Baker Labs; structure prediction, protein folding | , commercial or gratis | |||||||||
| FoldX | Energy calculations, protein design | , commercial or gratis | ||||||||||
| GROMACS | High performance MD | open source GNU GPL | ||||||||||
| GROMOS | Intended for biomolecules | , commercial | ||||||||||
| LAMMPS | Has potentials for soft and solid-state materials and coarse-grain systems | open source, GNU GPLv2 | ||||||||||
| MacroModel | OPLS-AA, MMFF, GBSA solvent model, conformational sampling, minimizing, MD. Includes the Maestro GUI which provides visualizing, molecule building, calculation setup, job launch and monitoring, project-level organizing of results, access to a suite of other modelling programs. | |||||||||||
| Materials Studio | Environment that brings materials simulation technology to desktop computing, solving key problems in R&D processes | , trial available | ||||||||||
| MBN Explorer + MBN Studio | Standard and reactive CHARMM force fields; molecular modeler ; explicit library of examples | , free trial available | ||||||||||
| MDynaMix | Parallel MD | open source GNU GPL | ||||||||||
| MOE | ||||||||||||
| ms2 | direct on the fly computation of large number of thermophysical properties. Main application of ms2 is on fluids. | open source | ||||||||||
| OpenMM | High Performance MD, highly flexible, Python scriptable | open source MIT | ||||||||||
| Orac | Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level | open source | ||||||||||
| NAMD + VMD | Fast, parallel MD, CUDA | , free academic use, source code | ||||||||||
| NWChem | High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM-MM methods | open source, Educational Community License version 2.0 | ||||||||||
| Protein Local Optimization Program | Helix, loop, and side chain optimizing, fast energy minimizing | |||||||||||
| Q | Free energy perturbation simulations, empirical valence bond, calculations of reaction free energies, linear interaction energy calculations of receptor-ligand binding affinities | open source GNU GPLv2 or later | ||||||||||
| QuantumATK | Complete atomistic modeling platform for material science. It includes DFT, Semi-empirical, and Force Field simulation engines. | , commercial | ||||||||||
| Quantum ESPRESSO | Open-source suite focused on electronic-structure calculations and MD, popular for its flexibility and extensive community support. | open source GNU GPLv2 or later | ||||||||||
| SAMSON | Computational nanoscience. Modular architecture, modules termed SAMSON Elements | , gratis | ||||||||||
| Scigress | MM, DFT, semiempirical methods, parallel MD, conformational analysis, Linear scaling SCF, docking protein-ligand, Batch processing, virtual screening, automated builders | |||||||||||
| Spartan | Small molecule MM and QM tools to determine conformation, structure, property, spectra, reactivity, and selectivity. | , free trial available | ||||||||||
| TeraChem | High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIA GPUs and 64-bit Linux, has heavily optimized CUDA code. | , trial licenses available | ||||||||||
| TINKER | Software tools for molecular design-Tinker-OpenMM Software tools for molecular design-Tinker-HP | , gratis | ||||||||||
| UCSF Chimera | Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development. | , free academic use | ||||||||||
| VASP | Highly efficient DFT code often used in materials science providing excellent performance on large systems. | |||||||||||
| YASARA | Molecular graphics, modeling, simulation |