List of software for molecular mechanics modeling
From Infogalactic: the planetary knowledge core
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
Min - Optimization, MD - Molecular Dynamics, MC - Monte Carlo, REM - Replica exchange method, QM - Quantum mechanics, Imp - Implicit water, GPU - GPU accelerated.
Y - Yes.
I - Has interface.
| Name | View
3D |
Model
Builder |
Min | MD | MC | REM | QM | Imp | GPU | Comments | License | Website |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Abalone | Y | Y | Y | Y | Y | Y | I | Y | Y | Biomolecular simulations, protein folding. | Proprietary, gratis | Agile Molecule |
| ACEMD[1] | Y | Y | Y | Y | Molecular dynamics with CHARMM, Amber forcefields. Running on NVIDIA GPUs. Heavily optimized with CUDA. | Proprietary. Gratis and commercial versions. | Acellera Ltd | |||||
| ADF | Y | Y | Y | Y | Y | Y | Y | ADF modeling suite: ReaxFF, UFF, QM/MM with Amber and Tripos force fields, DFT and Semi-empirical methods, conformational analysis with RDKit. ADF partially GPU-accelerated. | Proprietary, commercial. Gratis trial. | SCM | ||
| ADUN[2] | Y | Y | Y | Y | Y | Charmm, AMBER, user specified (through force field markup language, FFML), QM/MM calculations with Empirical Valence Bond (EVB); Framework based (GNUStep/cocoa); SCAAS for spherical boundary conditions | Free (GNU GPL) | https://gna.org/projects/adun | ||||
| AMBER[3] | Y | Y | Y | Y | I | Y | Y | Not free | ambermd.org | |||
| Ascalaph Designer | Y | Y | Y | Y | Y | Y | I | Y | Y | Molecular building (DNA, proteins, hydrocarbons, nanotubes). Molecular dynamics. GPU acceleration. |
Free (GNU GPL) & Commercial | Ascalaph Project |
| Automated Topology Builder (ATB) | Y | Y | Y | Automated molecular topology building service for small molecules (< 99 atoms). GROMOS, GROMACS, CNS formats with validation Repository for molecular topologies and pre-equilibrated systems |
Proprietary. Gratis for academic use and commercial. | Automated Topology Builder | ||||||
| Avogadro | Y | Y | Y | I | Molecule building, editing (Peptides, small molecules, crystals), Conformational analysis, 2D/3D conversion. Extensible interfaces to other tools. | Free (GNU GPL) | Avogadro | |||||
| BOSS | Y | Y | Y | OPLS | Commercial | Yale University | ||||||
| CHARMM | Y | Y | Y | Y | I | I | Y | Y | Commercial version with multiple graphical front ends is sold by Accelrys (as CHARMm) | Not free | charmm.org | |
| CHEMKIN | Chemical reaction kinetics. | Not free | CHEMKIN | |||||||||
| COSMOS | Y | Y | Y | Y | Y | I | Hybrid QM/MM COSMOS-NMR force field with fast semi-empirical calculation of electrostatic and/or NMR properties. 3-D graphical molecule builder and viewer. | Free(without GUI) and commercial | COSMOS Software | |||
| CP2K | Y | Y | Y | Y | Y | Y | CP2K can perform atomistic and molecular simulations of solid state, liquid and biological systems. | Free (GNU GPLv2 or later) | CP2K | |||
| Culgi | Y | Y | Y | Y | Y | Atomistic simulations and mesoscale methods. | Not free | Culgi BV | ||||
| Desmond | Y | Y | Y | Y | Y | Y | High Performance MD. Comes with a comprehensive GUI for building, visualizing, and reviewing results as well as calculation setup up and launching. | Proprietary. Gratis or commercial. | D. E. Shaw Research Schrödinger | |||
| Discovery Studio | Y | Y | Y | Y | Y | Y | Y | Discovery Studio is a comprehensive life science modeling and simulation suite of applications focused on optimizing the drug discovery process. Capabilities include, small molecule simulations, QM/MM, pharmacophore modeling, QSAR, protein-ligand docking, protein homology modeling, sequence analysis, protein-protein docking, antibody modeling, etc. | Closed source/Trial available | Accelrys | ||
| ENCAD | Y | Notably the first MD simulation software by Michael Levitt | Free | [1] | ||||||||
| fold.it | Y / I | Y | Y | Y | Y | Y | I | University of Washington and The Baker Labs. Structure prediction. Protein folding. | Proprietary. Gratis or commercial. | fold.it download page | ||
| FoldX | I | Y | Y | Energy calculations and protein design | Proprietary. Gratis or commercial. | CRG | ||||||
| GPIUTMD | I | I | Y | Y | I | Y | performs general purpose particle dynamics simulations on a single workstation, taking the advantage of NVIDIA CUDA GPUs. | Closed Source | http://gpiutmd.iut.ac.ir | |||
| GROMACS | Y | Y | I | Y[4] | Y | High performance MD | Free (GNU GPLv2) | gromacs.org | ||||
| GROMOS | Y | Y | Y | Y | Y | Y | Geared towards biomolecules | Proprietary, commercial | GROMOS Homepage | |||
| GULP | Y | Y | Molecular dynamics and Lattice optimization | Free for academic use | https://projects.ivec.org/gulp/ | |||||||
| HOOMD-blue | Y | Y | Y | General-purpose Molecular Dynamics highly optimized for GPUs. Includes various pair potentials, Brownian dynamics, dissipative particle dynamics, rigid body constraints, energy minimization, etc... | Free, open source | http://codeblue.umich.edu/hoomd-blue/index.html | ||||||
| ICM | Y | Y | Y | Y | I | Y | Powerful global optimizer in an arbitrary subset of internal variables, NOEs, Protein docking, Ligand docking, Peptide docking, EM, Density placement | Not free | Molsoft | |||
| LAMMPS | Y | Y | Y | Y | I | Y | Has potentials for soft and solid-state materials and coarse-grain systems | Free, Open Source. (GNU GPLv2) | Sandia | |||
| MacroModel | Y | Y | Y | Y | Y | I | Y | OPLS-AA, MMFF, GBSA solvent model, conformational sampling, minimization, MD. Includes the Maestro GUI which provides visualization, molecule building, calculation setup, job launching and monitoring, project-level organization of results and access to a suite of other modelling programs. | Commercial | Schrödinger | ||
| MAPS | Y | Y | Y | Y | Y | Y | Y | Building, visualization and analysis tools in a single user interface together with access to multiple simulation engines. | Closed source/Trial available | Scienomics | ||
| Materials Studio | Y | Y | Y | Y | Y | Y | Y | Y | Materials Studio is a software environment that brings the materials simulation technology to desktop computing, solving key problems throughout the R&D process. | Closed source/Trial available | Accelrys | |
| MedeA | Y | Y | Y | Y | Y | Y | MedeA combines leading experimental databases and major computational programs like the Vienna Ab-Initio Simulation Package (VASP), LAMMPS, GIBBS with sophisticated materials property prediction, analysis, and visualization. | Closed source/Trial available | Materials Design | |||
| MCCCS Towhee | Y | Originally designed for the prediction of fluid phase equilibria | Free (GNU GPL) | Towhee Project | ||||||||
| MDynaMix | Y | Parallel MD | Free (GNU GPL) | Stockholm University | ||||||||
| MOE | Y | Y | Y | Y | I | Y | Molecular Operating Environment | Commercial | Chemical Computing Group | |||
| MOIL | Y | Y | Y | Y | Also includes action-based algorithms (Stochastic Difference Equation in Time and Stochastic Difference Equation in Length) and locally enhanced sampling. | Free (public domain + source code) | link | |||||
| ORAC | Y | Y | Y | Y | A Molecular Dynamics Simulation Program to Explore Free Energy Surfaces in Biomolecular Systems at the Atomistic Level | Free, open source | ORAC download page | |||||
| NAB[5] | Y | Generation of Models for "Unusual" DNA and RNA | Free | Case group[dead link] | ||||||||
| NAMD + VMD | Y | Y | Y | Y | Y | Y | Y | Fast, parallel MD, CUDA | Open source, free to academics | Beckman Institute | ||
| NWChem | Y | Y | Y | High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM/MM methods | Open-source, Educational Community License version 2.0 | NWChem | ||||||
| Packmol | Y | Builds complex initial configurations for Molecular Dynamics | Free, Open Source. (GNU GPL) | link | ||||||||
| Prime | Y | Y | Y | Y | I | Y | Homology modeling, loop and side chain optimization, minimization, OPLS-AA, SGB solvent model, parallalized | Commercial | Schrödinger | |||
| Protein Local Optimization Program | Y | Y | Y | Y | Helix, loop, and side chain optimization. Fast energy minimization. | Not free | PLOP wiki | |||||
| Q | Y | (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. | Uppsala Molekylmekaniska HB | Q | ||||||||
| RedMD[6] | I | Y | Y | Y | Y | Reduced MD. Package for coarse-grained simulations. | Free on GNU Licence | University of Warsaw, ICM | ||||
| SAMSON | Y | Y | Y | Y | Y | Computational nanoscience (life sciences, materials, etc.). Modular architecture (SAMSON Elements are modules for SAMSON). | Proprietary, gratis | SAMSON Connect | ||||
| StruMM3D (STR3DI32) | Y | Y | Y | Y | ' | ' | Sophisticated 3-D molecule builder and viewer, advanced structural analytical algorithms, full featured molecular modeling and quantitation of stereo-electronic effects, docking and the handling of complexes. | The 200 atom version is free | Exorga, Inc. | |||
| SCIGRESS | Y | Y | Y | Y | Y | Y | MM, DFT, Semiempirical methods, parallel MD, conformational analysis, Linear scaling SCF, docking protein-ligand, Batch processing, Virtual screening, Automated builders (molecular dynamics, proteins, crystals) | Commercial | SCIGRESS.com | |||
| Spartan | Y | Y | Y | Y | Y | Y | Small molecule (< 2000 a.m.u.) MM and QM tools for determining conformation, structure, property, spectra, reactivity, and selectivity. | Commercial, Trial Available | Wavefunction, Inc. | |||
| TeraChem | Y | Y | Y | Y | High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. The software runs on NVIDIA GPUs and 64-bit Linux, and is based on heavily optimized CUDA code. | Closed source / Trial licenses available | PetaChem LLC | |||||
| TINKER | I | Y | Y | Y | Y | I | Y | Software tools for molecular design | Proprietary, gratis | Washington University | ||
| Tremolo-X | I | Y | Y | Fast, parallel MD | Not Free | Tremolo-X | ||||||
| UCSF Chimera | Y | Y | Y | Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development. | Free for academic use | University of California | ||||||
| VEGA ZZ | Y | Y | Y | I | Y | Y | Y | 3D viewer, multiple file format support, 2D and 3D editor, surface calculation, conformational analysis, MOPAC and NAMD interfaces, MD trajectory analysis, molecular docking, virtual screening, database engine, parallel design, OpenCL acceleration, etc. | Free for academic use | VEGA ZZ Web site | ||
| VLifeMDS | Y | Y | Y | Y | I | Y | Complete Molecular Modelling Software, QSAR, Combinatorial Library generation, Pharmacophore, Cheminformatics, docking, etc. | Not free | Vlife Sciences Technologies | |||
| WHAT IF | Y | Y | I | I | I | Visualizer for MD. Interface to GROMACS. | Not free | WHAT IF | ||||
| YASARA | Y | Y | Y | Y | Y | Molecular-graphics, -modeling and -simulation program | Not free | YASARA.org |
See also
- Molecular dynamics
- Molecular design software
- Molecule editor
- Molecular modeling on GPUs
- List of molecular graphics systems
- List of nucleic acid simulation software
- List of protein structure prediction software
- List of quantum chemistry and solid state physics software
- List of software for nanostructures modeling
- List of software for Monte Carlo molecular modeling
- Force field implementation
Notes and references
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- SINCRIS
- Linux4Chemistry
- Collaborative Computational Project
- World Index of Molecular Visualization Resources
- Short list of Molecular Modeling resources
- OpenScience
- Biological Magnetic Resonance Data Bank
- Materials modelling and computer simulation codes
- A few tips on molecular dynamics
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- ↑ Implicit Solvent - Gromacs
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