Comparison of software for molecular mechanics modeling

|{{No}}

|{{Yes}}

|{{Yes}}

|{{Yes}}

|{{Yes}}

|{{Yes}}

|{{some|I}}

|{{Yes}}

|{{Yes}}

|High Performance MD, Comprehensive analysis tools

|[https://ambermd.org/GetAmber.php#amber Proprietary], [https://ambermd.org/AmberTools.php Free open source]

|[https://ambermd.org/ AMBER MD]

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{some|I}}

| {{yes}}

| {{yes}}

| Biomolecular simulations, protein folding.

| {{proprietary}}, gratis, commercial

| [http://www.biomolecular-modeling.com/Abalone/ Agile Molecule]

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{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

| [https://www.scm.com SCM]

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{some|I}}

| {{yes}}

| {{yes}}

| Molecular building (DNA, proteins, hydrocarbons, nanotubes), molecular dynamics, GPU acceleration

| {{some|Mixed: free open source (GNU GPL) & commercial}}

| [http://www.biomolecular-modeling.com/Products.html Ascalaph Project]

| {{yes}}

| {{yes}}

| {{yes}}

| {{no}}

| {{no}}

| {{no}}

| {{some|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

| [http://avogadro.cc Avogadro]

| {{no}}

| {{no}}

| {{yes}}

| {{no}}

| {{yes}}

| {{no}}

| {{yes}}

| {{no}}

| {{no}}

| OPLS

| {{proprietary}}

| [http://zarbi.chem.yale.edu/software.html#boss Yale University]

| {{no}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{some|I}}

| {{some|I}}

| {{yes}}

| {{yes}}

|Commercial version with multiple graphical front ends is sold by BIOVIA (as CHARMm), formerly Accelrys.

| {{proprietary}}, commercial

| [https://web.archive.org/web/20090325101042/http://www.charmm.org/ charmm.org]

| {{no}}

| {{no}}

| {{no}}

| {{no}}

| {{no}}

| {{no}}

| {{no}}

| {{no}}

| {{no}}

| Chemical reaction kinetics.

| {{proprietary}}

| [http://www.reactiondesign.com/products/chemkin/chemkin-2/ CHEMKIN]

| {{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

| [http://cp2k.org/ CP2K]

| {{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

| [http://deshawresearch.com/resources.html D. E. Shaw Research] [https://web.archive.org/web/20130514084814/http://www.schrodinger.com/productpage/14/3/ Schrödinger]

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{no}}

| {{yes}}

| {{yes}}

| {{Yes}}

| 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

| [http://www.3dsbiovia.com/products/collaborative-science/biovia-discovery-studio/ Dassault Systèmes BIOVIA
(formerly Accelrys)]

| Y / I

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{some|I}}

| {{no}}

| {{no}}

| University of Washington and The Baker Labs; structure prediction, protein folding

| {{proprietary}}, commercial or gratis

| [http://fold.it/portal/ fold.it download page] {{Webarchive|url=https://web.archive.org/web/20110404020439/http://fold.it/portal/ |date=2011-04-04 }}

| {{some|I}}

| {{yes}}

| {{yes}}

| {{no}}

| {{no}}

| {{no}}

| {{no}}

| {{no}}

| {{no}}

| Energy calculations, protein design

| {{proprietary}}, commercial or gratis

| [http://foldx.crg.es/ CRG]

| {{no}}

| {{no}}

| {{yes}}

| {{yes}}

| {{no}}{{cite journal |vauthors=Harrison ET, Weidner T, Castner DG, Interlandi G |title=Predicting the orientation of protein G B1 on hydrophobic surfaces using Monte Carlo simulations |journal= Biointerphases |volume=12 |issue=2 | pages=02D401 |year=2017 |doi=10.1116/1.4971381|pmid=27923271 |pmc=5148762 }}

| {{yes}}

| {{some|I}}

| {{yes}}[http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent Implicit Solvent – Gromacs] {{webarchive |url=https://web.archive.org/web/20140729191820/http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent |date=July 29, 2014 }}

| {{yes}}

| High performance MD

| {{free}} open source GNU GPL

| [http://www.gromacs.org/ gromacs.org]

| {{no}}

| {{no}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| Intended for biomolecules

| {{proprietary}}, commercial

| [http://www.gromos.net/ GROMOS website]

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{some|I}}

| {{yes}}

| {{yes}}

| Has potentials for soft and solid-state materials and coarse-grain systems

| {{free}} open source, GNU GPLv2

| [http://lammps.sandia.gov/ Sandia]

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{no}}

| {{some|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}}

| [https://web.archive.org/web/20130203094650/http://www.schrodinger.com/productpage/14/11 Schrödinger]

| {{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

| [https://web.archive.org/web/20191128010114/https://www.scienomics.com/software/ Scienomics]

| {{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

| [http://www.3dsbiovia.com/products/collaborative-science/biovia-materials-studio/ Dassault Systèmes BIOVIA
(formerly Accelrys)]

| {{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

| [http://www.mbnresearch.com/ MBN Research Center]

| {{no}}

| {{no}}

| {{no}}

| {{yes}}

| {{no}}

| {{no}}

| {{no}}

| {{no}}

| {{no}}

| Parallel MD

| {{free}} open source GNU GPL

| [http://www.fos.su.se/~sasha/mdynamix/ Stockholm University]

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{no}}

| {{no}}

| {{some|I}}

| {{yes}}

| {{no}}

| [https://web.archive.org/web/20190113221313/http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm Molecular Operating Environment] (MOE)

| {{proprietary}}

| [http://www.chemcomp.com/ Chemical Computing Group]

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{no}}

| {{no}}

| {{no}}

| {{no}}

|On the fly calculation of large number of thermophysical properties. Main application is on fluids. |direct on the fly computation of large number of thermophysical properties. Main application of ms2 is on fluids.

| {{free}} open source

|[https://www.ms-2.de/home.html ms-2.de]

|{{No}}

|{{No}}

|{{Yes}}

|{{Yes}}

|{{Yes}}

|{{Yes}}

|{{No}}

|{{Yes}}

|{{Yes}}

|High Performance MD, highly flexible, Python scriptable

| {{free}} open source MIT

|[https://openmm.org/ OpenMM]

| {{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

| [http://www.chim.unifi.it/orac Orac download page]

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{no}}

| {{yes}}

| {{some|I}}

| {{yes}}

| {{yes}}

| Fast, parallel MD, CUDA

| {{proprietary}}, free academic use, source code

| [http://www.ks.uiuc.edu/Research/vmd/ Beckman Institute]

| {{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

| [https://nwchemgit.github.io/ NWChem]

| {{no}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{no}}

| {{no}}

| {{no}}

| {{no}}

| Helix, loop, and side chain optimizing, fast energy minimizing

| {{proprietary}}

| [http://wiki.jacobsonlab.org/index.php/Main_Page PLOP wiki]

| {{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

| {{free}} open source GNU GPLv2 or later

| [http://xray.bmc.uu.se/~aqwww/q Q]

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{No}}

| {{yes}}

| {{yes}}

| {{yes}}

| Complete atomistic modeling platform for material science. It includes DFT (Plane-Wave and LCAO), Semi-empirical, and Force Field simulation engines.

| {{proprietary}}, commercial

| [https://www.synopsys.com/silicon/quantumatk.html Synopsys QuantumATK]

| {{no}}

| {{no}}

| {{yes}}

| {{yes}}

| {{no}}

| {{no}}

| {{yes}}

| {{some|I}}

| {{yes}}

| Open-source suite focused on electronic-structure calculations and MD (particularly CPMD), popular for its flexibility and extensive community support.

| {{free}} open source GNU GPLv2 or later

| [https://www.quantum-espresso.org/ Quantum ESPRESSO]

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{no}}

| {{no}}

| {{yes}}

| {{no}}

| {{no}}

| Computational nanoscience (life sciences, materials, etc.). Modular architecture, modules termed SAMSON Elements

| {{proprietary}}, gratis

| [https://www.samson-connect.net SAMSON Connect]

| {{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}}

| [http://www.scigress.com/ SCIGRESS.com]

| {{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

| [http://www.wavefun.com/products/spartan.html Wavefunction, Inc.]

| {{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

| [http://petachem.com/ PetaChem LLC]

| {{some|I}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{some|I}}

| {{some|I}}

| {{yes}}

| {{yes}}

| Software tools for molecular design-Tinker-OpenMM{{cite journal |author1=M. Harger |author2=D. Li |author3=Z. Wang |author4=K. Dalby |author5=L. Lagardère |author6=J.-P. Piquemal |author7=J. Ponder |author8=P. Ren |title= Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs |journal= Journal of Computational Chemistry | pages=2047–2055 | volume = 38 |issue= 23 |year=2017 |doi=10.1002/jcc.24853 |pmid= 28600826 |pmc= 5539969 }}

Software tools for molecular design-Tinker-HP{{cite journal |author1=L. Lagardère |author2=L.-H. Jolly |author3=F. Lipparini |author4=F. Aviat |author5=B. Stamm |author6=Z. F. Jing |author7=M. Harger |author8=H. Torabifard |author9=G. A. Cisneros |author10=M. J. Schnieders |author11=N. Gresh |author12=Y. Maday |author13=P. Y. Ren |author14=J. W. Ponder |author15=J.-P. Piquemal |title= Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields |journal= Chemical Science | pages=956–972 | volume = 9 |issue= 4 |year=2018 |doi=10.1039/C7SC04531J |pmid= 29732110 |pmc= 5909332 }}

| {{proprietary}}, gratis

| [http://dasher.wustl.edu/tinker/ Washington University]

| {{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

| [http://www.cgl.ucsf.edu/chimera/ University of California]

| {{no}}

| {{no}}

| {{yes}}

| {{yes}}

| {{no}}

| {{yes}}

| {{yes}}

| {{some|I}}

| {{yes}}

| Highly efficient DFT code often used in materials science providing excellent performance on large systems.

| {{proprietary}}

| [https://www.vasp.at/ VASP]

| {{yes}}

| {{yes}}

| {{yes}}

| {{yes}}

| {{no}}

| {{no}}

| {{yes}}

| {{no}}

| {{yes}}

| Molecular graphics, modeling, simulation

| {{proprietary}}

| [http://www.yasara.com/ YASARA.org]