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| {{free}} [[open source]], public domain, source code
| {{free}} [[open source]], public domain, source code
| [http://cbsu.tc.cornell.edu/software/moil/moil.html link]
| [http://cbsu.tc.cornell.edu/software/moil/moil.html link]
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| MolMeccano
| {{no}}
| {{yes}}
| {{no}}
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| {{no}}
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| Semi-automatic Force Field parametrizer
| {{proprietary}}
| [http://www.molmeccano.com/index.html MolMeccano Project]
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| [[Orac (MD program)|Orac]]
| [[Orac (MD program)|Orac]]

Revision as of 04:37, 16 August 2017

This is a list of computer programs that are predominantly used for molecular mechanics calculations.

2
Name View 3D Model builder Min MD MC REM QM Imp GPU Comments License Website
Abalone Yes Yes Yes Yes Yes Yes I Yes Yes Biomolecular simulations, protein folding. Proprietary, gratis Agile Molecule
ACEMD[1] No No Yes Yes No Yes No No Yes Molecular dynamics with CHARMM, Amber forcefields; runs on NVIDIA GPUs, highly optimized with CUDA Proprietary, gratis and commercial versions Acellera Ltd
ADF Yes Yes Yes Yes No 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
ADUN[2] No No Yes Yes No No Yes Yes Yes Charmm, AMBER, user specified (via force field markup language, FFML), QM-MM calculations with empirical valence bond (EVB); framework based (GNUStep-Cocoa); SCAAS for spherical boundary conditions Free open source GNU GPL https://gna.org/projects/adun
Assisted Model Building with Energy Refinement (AMBER)[3] No Yes Yes Yes No Yes I Yes Yes ? Proprietary ambermd.org
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
Automated Topology Builder (ATB) Yes Yes Yes No No No No No No Automated molecular topology building service for small molecules (< 99 atoms). GROMOS, GROMACS, CNS, LAMMPS formats with validation
Repository for molecular topologies and pre-equilibrated systems 		Proprietary commercial, gratis academic use Automated Topology Builder
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 Accelrys (as CHARMm) Proprietary, commercial charmm.org
CHEMKIN No No No No No No No No No Chemical reaction kinetics. Proprietary CHEMKIN
COSMOS Yes Yes Yes Yes Yes No I No No 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 Proprietary, commercial, free without GUI COSMOS Software
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
Culgi Yes Yes Yes Yes Yes No I No No Atomistic simulations and mesoscale methods, database integration, mapping techniques, interface to MOPAC/NWChem Proprietary Culgi BV
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 No 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 Accelrys
DL_POLY
DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.
Energy Calculation and Dynamics (ENCAD) No No No Yes No No No No No Notably the first MD simulation software by Michael Levitt Free open source [1]
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
FoldX I Yes Yes No No No No No No Energy calculations, protein design Proprietary, commercial or gratis CRG
GPIUTMD I I Yes Yes No I No No Yes Performs general purpose particle dynamics simulations on a single workstation, exploiting NVIDIA CUDA GPUs Proprietary http://gpiutmd.iut.ac.ir
GROMACS No No No Yes No Yes I Yes[4] Yes High performance MD Free open source GNU GPL gromacs.org
GROMOS No No Yes Yes Yes Yes No Yes Yes Intended for biomolecules Proprietary, commercial GROMOS website
GULP No No Yes Yes No No No No No Molecular dynamics and lattice optimization Proprietary, free academic use https://web.archive.org/web/20110604021055/http://projects.ivec.org/gulp/
HOOMD-blue No No Yes Yes Yes No No No Yes General-purpose molecular dynamics highly optimized for GPUs, includes various pair potentials, Brownian dynamics, dissipative particle dynamics, rigid body constraints, energy minimizing, etc. Free open source http://glotzerlab.engin.umich.edu/hoomd-blue/
ICM Yes Yes Yes No Yes No I Yes No Powerful global optimizer in an arbitrary subset of internal variables, NOEs, docking (protein, ligand, peptide), EM, density placement Proprietary Molsoft
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 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 Accelrys
MedeA Yes Yes Yes Yes Yes No Yes No No Combines leading experimental databases and major computational programs like the Vienna Ab-initio Simulation Package (VASP), LAMMPS, GIBBS with sophisticated materials property prediction, analysis, visualizing Proprietary, trial available Materials Design
MCCCS Towhee No No No No Yes No No No No Originally designed to predict fluid phase equilibria Free open source GNU GPL Towhee Project
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
MOIL Yes Yes Yes Yes No Yes No No Yes Includes action-based algorithms (stochastic difference equations in time, length) and locally enhanced sampling Free open source, public domain, source code link
MolMeccano No Yes No No No No No No No Semi-automatic Force Field parametrizer Proprietary MolMeccano Project
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
NAB[5] No Yes No No No No No No No Generates models for unusual DNA and RNA Free open source Case group
NAMD + VMD Yes Yes Yes Yes No Yes No 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
Packmol No Yes No No No No No No No Builds complex initial configurations for molecular dynamics Free open source GNU link
Prime Yes Yes Yes No Yes No I Yes No Homology modeling, loop and side chain optimizing, minimizing, OPLS-AA, SGB solvent model, parallalized Proprietary Schrödinger
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 Uppsala Molekylmekaniska HB Q
RedMD[6] I Yes Yes Yes Yes No No No No Reduced MD, package for coarse-grained simulations Free, open source GNU University of Warsaw, ICM
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
StruMM3D (STR3DI32) Yes Yes Yes Yes No No No No No Sophisticated 3-D molecule builder and viewer, advanced structural analytical algorithms, full featured molecular modeling and quantitation of stereo-electronic effects, docking, and handling of complexes. Proprietary, free 200 atom version Exorga, Inc.
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[7] Proprietary, gratis Washington University
Tremolo-X I No Yes Yes No No No No No Fast, parallel MD Proprietary Tremolo-X
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
VEGA ZZ Yes Yes Yes I Yes No No Yes Yes 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. Proprietary, free academic use VEGA ZZ website
VLifeMDS Yes Yes Yes No Yes No I No Yes Complete molecular modelling software, QSAR, combinatorial library generation, pharmacophore, cheminformatics, docking, etc. Proprietary Vlife Sciences Technologies
WHAT IF Yes Yes I I I No No No No Visualizer for MD, interface to GROMACS Proprietary WHAT IF
YASARA Yes Yes Yes Yes No No Yes No Yes Molecular graphics, modeling, simulation Proprietary YASARA.org

See also

Notes and references

  1. ^ 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.
  2. ^ 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)
  3. ^ 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.
  4. ^ Implicit Solvent - Gromacs Archived July 29, 2014, at the Wayback Machine
  5. ^ Macke T, Case DA (1998). "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379–393.
  6. ^ A. Górecki; M. Szypowski; M. Długosz; J. Trylska (2009). "RedMD - Reduced molecular dynamics package". J. Comp. Chem. 30 (14): 2364–2373. doi:10.1002/jcc.21223. PMID 19247989.
  7. ^ 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. doi:10.1002/jcc.24853.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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