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, 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. | Free | Agile Molecule |
| ACEMD[1] | Y | 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 | 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 (licensed under GNU GPL) | adun.imim.es | ||||
| 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 |
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 (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 kintetics. | 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. | Free and 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 | ||
| fold.it | Y / I | Y | Y | Y | Y | Y | I | University of Washington and The Baker Labs. Structure prediction. Protein folding. | Free, download | fold.it download page | ||
| FoldX | I | Y | Y | Energy calculations and protein design | Free for academic use | 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 | Not free | 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 | Towhee Project | ||||||||
| MDynaMix | 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 | |||||
| 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 | ||||||||
| 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 | ||||
| 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 | Free | 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. | 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, Combinetorial 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
- ^ 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 (19): 5179–5197. doi:10.1021/ja00124a002.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent
- ^ 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)