Comparison of software for molecular mechanics modeling
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,
HA - Hardware accelerated.
Y - Yes.
I - Has interface.
| Name | View
3D |
Model
Builder |
Min | MD | MC | REM | QM | Imp | HA | Comments | License | Website |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Abalone | Y | Y | Y | Y | Y | Y | I | Y | Y | Biomolecular simulations, protein folding. | Free | Agile Molecule |
| ACEMD[1] | Y | Y | Y | Molecular dynamics with CHARMM, Amber forcefields. Running on NVIDIA GPUs. Heavily optimized with CUDA. | Basic version free. Commercial version available. | Acellera Ltd | ||||||
| ADUN[2] | 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 | adun.imim.es | |||||
| AMBER[3] | Y | Y | Y | Y | Y | Not free | ambermd.org | |||||
| Ascalaph Designer | Y | Y | Y | Y | I | Y | Y | Molecular building (DNA, proteins, hydrocarbons, nanotubes). Molecular dynamics. GPU acceleration. |
Free & Commercial | Ascalaph Project | ||
| Automated Topology Builder (ATB) | 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 |
Free for academic use | 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, open source | Avogadro | |||||
| Balloon | Y | Y | 2D/3D conversion and conformational analysis. | Free to use, closed source | Åbo Akademi | |||||||
| BOSS | Y | Y | Y | OPLS | Commercial | Yale University | ||||||
| CHARMM | Y | Y | Y | Y | I | I | Y | Commercial version with multiple graphical front ends is sold by Accelrys (as CHARMm) | Not free | charmm.org | ||
| Chemitorium | Y | Y | Free 2D/3D graphical organic molecule builder, viewer and visualisation tool. | Free | link | |||||||
| ChemSketch | Y | Y | Y | Fast 2-D graphical molecule builder and 3-D viewer. Contains simplified CHARMM for fast stable inaccurate optimization of single molecules up to 1000 atoms | Advanced Chemistry Development, Inc. | |||||||
| 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 | |||
| Culgi | Y | Y | Y | Y | Y | Atomistic simulations and mesoscale methods. | Not free | Culgi BV | ||||
| Desmond | Y | Y | Y | High Performance MD. | Free and commercial | D. E. Shaw Research | ||||||
| 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 | ||
| FoldX | I | Y | Y | Energy calculations and protein design | Free for academic use | CRG | ||||||
| GoVASP | Y | I | I | I | GoVASP is a sophisticated graphical user interface for the Vienna Ab-Initio Simulation Package (VASP). GoVASP comprises tools to prepare, perform and monitor VASP calculations and to evaluate and visualize the computed data. | Closed source/Not free/Trial available | Windiks Consulting | |||||
| GROMACS | Y | Y | ? | High performance MD | Free | gromacs.org | ||||||
| GROMOS | Y | Y | Geared towards biomolecules | Not free | GROMOS Homepage | |||||||
| ICM | Y | Y | Y | Y | 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 | I | Y | Has potentials for soft and solid-state materials and coarse-grain systems | Free | Sandia | ||||
| MacroModel | Y | Y | Y | Y | Y | I | Y | OPLS-AA, GBSA solvent model, conformational sampling, minimization, MD | Not free | Schrödinger, LLC | ||
| 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) with sophisticated materials property prediction, analysis, and visualization. | Closed source/Not free | link | |||
| MCCCS Towhee | Y | Originally designed for the prediction of fluid phase equilibria | Free | Towhee Project | ||||||||
| MDynaMix[4] | Y | Parallel MD | Free | 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 | link | |||||
| molecools | Y | Y | Simple Javascript molecular visualization tool | link | ||||||||
| MOLDY | Y | Parallel, only pair-potentials, Cell lists, modified Beeman's algorithm | Free | Moldy | ||||||||
| ORAC | 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 | ||||||||
| Packmol | Y | Builds complex initial configurations for Molecular Dynamics | link | |||||||||
| Prime | Y | Y | Y | Y | I | Y | Homology modeling, loop and side chain optimization, minimization, OPLS-AA, SGB solvent model, parallalized | link | ||||
| Protein Local Optimization Program | Y | Y | Y | Y | Helix, loop, and side chain optimization. Fast energy minimization. | Not free | link | |||||
| p4vasp | Y | Y | Python-based viewer, structure builder and VASP results browser. Shows band-structure, charge densities and simulates STM images. | Free, open source | Download at [1], Original web [2] | |||||||
| PyMol | Y | Y | Python-based viewer, many plugins to other software. Some mutagenisis. | Free, open source | [3] | |||||||
| QMOL | Y | Protein viewer, provided by DNASTAR | Free | DNASTAR, Inc. | ||||||||
| RasMol | Y | Fast viewer | Free | RasMol | ||||||||
| Raster3D | Y | High quality raster images | Free | University of Washington | ||||||||
| RedMD[6] | I | Y | Y | Y | Y | Reduced MD. Package for coarse-grained simulations. | Free on GNU Licence | University of Warsaw, ICM | ||||
| 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. | |||
| Selvita Protein Modeling Platform | Y | Y | Y | Y | Protein structure prediction, homology modeling, ab initio modeling, loop modeling, protein threading | Commercial | Selvita Ltd | |||||
| SimBioSys' MoDeST (Molecular Design Software Toolkit) | Y | Y | Y | Y | molecular docking, scoring functions for docking, "ligand-based", "fragment-based", "de-novo" | Not Free | SimBioSys Inc. | |||||
| Spartan | Y | Y | Y | Y | Y | Y | Small molecule (< 2000 a.m.u.) MM and QM tools for determining conformation, structure, property, specra, reactivity, and selectivity. | Commercial, Trial Available | Wavefunction, Inc. | |||
| SwissParam | Web server to determine automatically parameters and topologies for small organic molecules, for use with the CHARMM all atoms force field. Files can be used with CHARMM and GROMACS. | Free for academic. CHARMm licence required for commercial usage. | SwissParam. | |||||||||
| TeraChem [7] | 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 | Free | Washington University | ||
| UCSF Chimera | Y | Y | Y | Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development. | University of California | |||||||
| VLifeMDS | Y | Y | Y | Y | I | Y | Complete Molecular Modelling Software, QSAR, Combinetorial Library generation, Pharmacophore, Cheminformatics, docking, etc. | Not free | Vlife Sciences Technologies | |||
| VMD + NAMD | Y | Y | Y | Y | Y | Fast, parallel MD | Free | Beckman Institute | ||||
| WHAT IF | Y | Y | I | I | I | Visualizer for MD. Interface to GROMACS. | Not free | WHAT IF | ||||
| xeo | Y | Y | open project management for nanostructures | link | ||||||||
| YASARA | Y | Y | Y | Y | Molecular-graphics, -modeling and -simulation program | Not free | YASARA.org | |||||
| Zodiac | Y | Y | Y | Drug design suite | link |
See also
- ChemSpider
- Molecular dynamics
- Molecular design software
- Molecule editor
- Molecular modeling on GPU
- 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
- List of web resources for visualizing molecular dynamics
- Force field implementation
References
- ^ M. J. Harvey, G. Giupponi and G. De Fabritiis (2009). "ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale". Journal of Chemical Theory and Computation. 5 (6): 1632–1639. doi:10.1021/ct9000685.
- ^ Johnston, MA, Fernández-Galván, I, Villà-Freixa, J (2005). "Framework-based design of a new all-purpose molecular simulation application: the Adun simulator". J. Comp. Chem. 26 (15): 1647–1659. doi:10.1002/jcc.20312. PMID 16175583.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995). "A second generation force field for the simulation of proteins, nucleic acids, and organic molecules". J. Am. Chem. Soc. 117: 5179–5197. doi:10.1021/ja00124a002.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Lyubartsev AP, Laaksonen A (2000). "MDynaMix - A scalable portable parallel MD simulation package for arbitrary molecular mixtures". Computer Physics Communications. 128: 565–589. doi:10.1016/S0010-4655(99)00529-9.
- ^ Macke T, Case DA (1998). "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379–393.
- ^ A. Górecki, M. Szypowski, M. Długosz and J. Trylska (2009). "RedMD - Reduced molecular dynamics package". J. Comp. Chem. 30 (14): 2364–2373. doi:10.1002/jcc.21223. PMID 19247989.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ JCTC citation needed.