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, commercial | 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[permanent dead link] |
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 sourceGNU GPL | https://web.archive.org/web/20160303133843/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 | Proprietarycommercial, 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 sourceGNU 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 |
ChemDoodle 3D | Yes | Yes | Yes | No | No | No | No | No | No | Intuitive building of molecules in real-time; production of high quality publication graphics; works on Windows, macOS and Linux; developed by iChemLabs | Proprietary, commercial, free trial | ChemDoodle 3D Website |
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 sourceGNU GPLv2 or later | CP2K |
Culgi | Yes | Yes | Yes | Yes | Yes | No | Yes | Yes | No | Atomistic and coarse-grained simulations, mesoscale methods, COSMO-RS and UNIFAC, database integration, mapping techniques, AM1 and interface to MOPAC/NWChem | Proprietarycommercial, gratis academic education | 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 | |
DFTB+ | No | No | Yes | No | No | No | No | No | No | A fast and efficient versatile quantum mechanical simulation software package. Using DFTB+ you can carry out quantum mechanical simulations similar to density functional theory but in an approximate way, typically gaining around two orders of magnitude in speed. | Free open sourceGNU LGPL | [1] |
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 | Dassault Systèmes BIOVIA (formerly Accelrys) |
DL_POLY | No | Yes | Yes | Yes | No | No | I | No | No | DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith. It is part of the DL_Software suite of projects including DL_MESO (DPD), DL_FIELD (FF builder), ChemShell (QMMM environment), etc. | Proprietarycommercial, free source for academic use | DL_POLY |
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 | [2] |
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 |
GOMC | No | No | No | No | Yes | Yes | No | No | Yes | GPU Optimized Monte Carlo. Atomistic simulation engine, capable of simulating complex systems. | Free opensource.GNU Affero General Public License. | GOMC website. GOMC Github |
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 | Yes | Yes | No[4] | Yes | I | Yes[5] | Yes | High performance MD | Free open sourceGNU 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 | http://gulp.curtin.edu.au/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/ |
HyperChem | Yes | Yes | Yes | Yes | Yes | No | Yes | Yes | No | De Facto Standard Molecular Modeling System | Proprietary | Hypercube, Inc. |
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[6] | 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[7] + 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 |
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 sourceGNU GPL | Towhee Project |
MDynaMix | No | No | No | Yes | No | No | No | No | No | Parallel MD | Free open sourceGNU 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 | MOIL |
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[8] | 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 | 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 |
Packmol | No | Yes | No | No | No | No | No | No | No | Builds complex initial configurations for molecular dynamics | Free open sourceGNU | 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[9] | I | Yes | Yes | Yes | Yes | No | No | No | No | Reduced MD, package for coarse-grained simulations | Free, open sourceGNU | 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 performanceGPU-accelerated ab initiomolecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIAGPUs and 64-bitLinux, 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[10] Software tools for molecular design-Tinker-HP[11] | 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 |