Global InformationComparison of software for molecular mechanics modeling information
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
- GPU – GPU accelerated
- I – Has interface
- Imp – Implicit water
- MC – Monte Carlo
- MD – Molecular dynamics
- Min – Optimization
- QM – Quantum mechanics
- REM – Replica exchange method
| Name | View 3D | Model builder | Min | MD | MC | REM | QM | Imp | GPU | Comments | License | Website |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AMBER[1] | No | Yes | Yes | Yes | Yes | Yes | I | Yes | Yes | High Performance MD, Comprehensive analysis tools | Proprietary, Free open source | AMBER MD |
| Abalone | Yes | Yes | Yes | Yes | Yes | Yes | I | Yes | Yes | Biomolecular simulations, protein folding. | Proprietary, gratis, commercial | Agile Molecule |
| ADF | Yes | Yes | Yes | Yes | Yes | No | Yes | Yes | Yes | Modeling suite: ReaxFF, UFF, QM-MM with Amber and Tripos force fields, DFT and semi-empirical methods, conformational analysis with RDKit; partly GPU-accelerated | Proprietary, commercial, gratis trial | SCM |
| Ascalaph Designer | Yes | Yes | Yes | Yes | Yes | Yes | I | Yes | Yes | Molecular building (DNA, proteins, hydrocarbons, nanotubes), molecular dynamics, GPU acceleration | Mixed: free open source (GNU GPL) & commercial | Ascalaph Project |
| Avogadro | Yes | Yes | Yes | No | No | No | I | No | No | Molecule building, editing (peptides, small molecules, crystals), conformational analysis, 2D/3D conversion; extensible interfaces to other tools | Free open source GNU GPL | Avogadro |
| BOSS | No | No | Yes | No | Yes | No | Yes | No | No | OPLS | Proprietary | Yale University |
| CHARMM | No | Yes | Yes | Yes | Yes | I | I | Yes | Yes | Commercial version with multiple graphical front ends is sold by BIOVIA (as CHARMm), formerly Accelrys. | Proprietary, commercial | charmm.org |
| CHEMKIN | No | No | No | No | No | No | No | No | No | Chemical reaction kinetics. | Proprietary | CHEMKIN |
| CP2K | No | No | Yes | Yes | Yes | No | Yes | Yes | Yes | CP2K can perform atomistic and molecular simulations of solid state, liquid and biological systems. | Free open source GNU GPLv2 or later | CP2K |
| Desmond | Yes | Yes | Yes | Yes | No | Yes | No | No | Yes | High performance MD; has comprehensive GUI to build, visualize, and review results and calculation setup up and launch | Proprietary, commercial or gratis | D. E. Shaw Research Schrödinger |
| Discovery Studio | Yes | Yes | Yes | Yes | Yes | No | Yes | Yes | Yes | 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. | Proprietary, trial available | Dassault Systèmes BIOVIA (formerly Accelrys) |
| fold.it | Y / I | Yes | Yes | Yes | Yes | Yes | I | No | No | University of Washington and The Baker Labs; structure prediction, protein folding | Proprietary, commercial or gratis | fold.it download page Archived 2011-04-04 at the Wayback Machine |
| FoldX | I | Yes | Yes | No | No | No | No | No | No | Energy calculations, protein design | Proprietary, commercial or gratis | CRG |
| GROMACS | No | No | Yes | Yes | No[2] | Yes | I | Yes[3] | Yes | High performance MD | Free open source GNU GPL | gromacs.org |
| GROMOS | No | No | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Intended for biomolecules | Proprietary, commercial | GROMOS website |
| LAMMPS | Yes | Yes | Yes | Yes | Yes | Yes | I | Yes | Yes | Has potentials for soft and solid-state materials and coarse-grain systems | Free open source, GNU GPLv2 | Sandia |
| MacroModel | Yes | Yes | Yes | Yes | Yes | No | I | Yes | No | 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. | Proprietary | Schrödinger |
| MAPS[4] | Yes | Yes | Yes | Yes | Yes | Yes | Yes | No | Yes | Building, visualizing, and analysis tools in one user interface, with access to multiple simulation engines | Proprietary, trial available | Scienomics |
| Materials Studio | Yes | Yes | Yes | Yes | Yes | No | Yes | Yes | Yes | Environment that brings materials simulation technology to desktop computing, solving key problems in R&D processes | Proprietary, trial available | Dassault Systèmes BIOVIA (formerly Accelrys) |
| MBN Explorer[5] + MBN Studio | Yes | Yes | Yes | Yes | Yes | No | No | Yes | Yes | Standard and reactive CHARMM force fields; molecular modeler (carbon nanomaterials, biomolecules, nanocrystals); explicit library of examples | Proprietary, free trial available | MBN Research Center |
| MDynaMix | No | No | No | Yes | No | No | No | No | No | Parallel MD | Free open source GNU GPL | Stockholm University |
| MOE | Yes | Yes | Yes | Yes | No | No | I | Yes | No | Molecular Operating Environment (MOE) | Proprietary | Chemical Computing Group |
| ms2 | Yes | Yes | Yes | Yes | Yes | No | No | No | No | direct on the fly computation of large number of thermophysical properties. Main application of ms2 is on fluids. | Free open source | ms-2.de |
| OpenMM | No | No | Yes | Yes | Yes | Yes | No | Yes | Yes | High Performance MD, highly flexible, Python scriptable | Free open source MIT | OpenMM |
| Orac | No | No | Yes | Yes | No | Yes | No | Yes | No | Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level | Free open source | Orac download page |
| NAMD + VMD | Yes | Yes | Yes | Yes | No | Yes | I | Yes | Yes | Fast, parallel MD, CUDA | Proprietary, free academic use, source code | Beckman Institute |
| NWChem | No | No | Yes | Yes | No | No | Yes | No | No | High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM-MM methods | Free open source, Educational Community License version 2.0 | NWChem |
| Protein Local Optimization Program | No | Yes | Yes | Yes | Yes | No | No | No | No | Helix, loop, and side chain optimizing, fast energy minimizing | Proprietary | PLOP wiki |
| Q | No | No | No | Yes | No | No | No | No | No | (I) Free energy perturbation (FEP) simulations, (II) empirical valence bond (EVB), calculations of reaction free energies, (III) linear interaction energy (LIE) calculations of receptor-ligand binding affinities | Free open source GNU GPLv2 or later | Q |
| QuantumATK | Yes | Yes | Yes | Yes | Yes | No | Yes | Yes | No | Complete atomistic modeling platform for material science. It includes DFT (Plane-Wave and LCAO), Semi-empirical, and Force Field simulation engines. | Proprietary, commercial | Synopsys QuantumATK |
| SAMSON | Yes | Yes | Yes | Yes | No | No | Yes | No | No | Computational nanoscience (life sciences, materials, etc.). Modular architecture, modules termed SAMSON Elements | Proprietary, gratis | SAMSON Connect |
| Scigress | Yes | Yes | Yes | Yes | No | No | Yes | Yes | No | MM, DFT, semiempirical methods, parallel MD, conformational analysis, Linear scaling SCF, docking protein-ligand, Batch processing, virtual screening, automated builders (molecular dynamics, proteins, crystals) | Proprietary | SCIGRESS.com |
| Spartan | Yes | Yes | Yes | No | Yes | No | Yes | Yes | No | Small molecule (< 2,000 a.m.u.) MM and QM tools to determine conformation, structure, property, spectra, reactivity, and selectivity. | Proprietary, free trial available | Wavefunction, Inc. |
| TeraChem | No | No | Yes | Yes | No | No | Yes | No | Yes | 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. | Proprietary, trial licenses available | PetaChem LLC |
| TINKER | I | Yes | Yes | Yes | Yes | I | I | Yes | Yes | Software tools for molecular design-Tinker-OpenMM[6]
Software tools for molecular design-Tinker-HP[7] |
Proprietary, gratis | Washington University |
| UCSF Chimera | Yes | Yes | Yes | No | No | No | No | No | No | Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development. | Proprietary, free academic use | University of California |
| YASARA | Yes | Yes | Yes | Yes | No | No | Yes | No | Yes | Molecular graphics, modeling, simulation | Proprietary | YASARA.org |
- ^ "Citations for Amber". ambermd.org. Retrieved 2021-06-15.
- ^ Harrison ET, Weidner T, Castner DG, Interlandi G (2017). "Predicting the orientation of protein G B1 on hydrophobic surfaces using Monte Carlo simulations". Biointerphases. 12 (2): 02D401. doi:10.1116/1.4971381. PMC 5148762. PMID 27923271.
- ^ Implicit Solvent – Gromacs Archived July 29, 2014, at the Wayback Machine
- ^ "MAPS". Archived from the original on 2019-11-28. Retrieved 2016-11-14.
- ^ I.A. Solov'yov; A.V. Yakubovich; P.V. Nikolaev; I. Volkovets; A.V. Solov'yov (2012). "MesoBioNano Explorer - A universal program for multiscale computer simulations of complex molecular structure and dynamics". J. Comput. Chem. 33 (30): 2412–2439. doi:10.1002/jcc.23086. PMID 22965786. S2CID 22553279.
- ^ M. Harger; D. Li; Z. Wang; K. Dalby; L. Lagardère; J.-P. Piquemal; J. Ponder; P. Ren (2017). "Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs". Journal of Computational Chemistry. 38 (23): 2047–2055. doi:10.1002/jcc.24853. PMC 5539969. PMID 28600826.
- ^ L. Lagardère; L.-H. Jolly; F. Lipparini; F. Aviat; B. Stamm; Z. F. Jing; M. Harger; H. Torabifard; G. A. Cisneros; M. J. Schnieders; N. Gresh; Y. Maday; P. Y. Ren; J. W. Ponder; J.-P. Piquemal (2018). "Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields". Chemical Science. 9 (4): 956–972. doi:10.1039/C7SC04531J. PMC 5909332. PMID 29732110.