Comparison of software for molecular mechanics modeling. This is a list of computer programs that are predominantly used for molecular mechanics calculations. Name. View 3. DModel builder. Min. MDMCREMQMImp. Free Molecular Dynamics Simulation Software' title='Free Molecular Dynamics Simulation Software' />GPUComments. License. Website. Abalone. Yes. Yes. Yes. Yes. Yes. Yes. IYes. Yes. Biomolecular simulations, protein folding. Proprietary, gratis, commercial. Agile Molecule. ACEMD1No. Gary Scotts collection of source code links. CHARMM Chemistry at HARvard Macromolecular Mechanics A molecular simulation program with broad application to manyparticle systems with a comprehensive set of. No. Yes. Yes. No. Yes. No. No. Yes. RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/Articleimage/2017/AY/c7ay00838d/c7ay00838d-f8_hi-res.gif' alt='Free Molecular Dynamics Simulation Software' title='Free Molecular Dynamics Simulation Software' />Molecular dynamics with CHARMM, Amber forcefields runs on NVIDIA GPUs, highly optimized with CUDAProprietary, gratis and commercial versions. Acellera Ltd. ADFYes. Yes. Yes. Yes. No. No. Yes. Yes. Yes. Modeling suite Reax. FF, 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. SCMADUN2No. 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 GPLhttps web. Free Molecular Dynamics Simulation Software' title='Free Molecular Dynamics Simulation Software' />Assisted Model Building with Energy Refinement AMBER3No. Yes. Yes. Yes. No. Yes. IYes. Yes Proprietaryambermd. Ascalaph Designer. Yes. Yes. Yes. Yes. Yes. Yes. IYes. Yes. Molecular building DNA, proteins, hydrocarbons, nanotubes, molecular dynamics, GPU acceleration. Mixed free open source GNU GPL commercial. Ascalaph Project. I Technical Challenges for Diamond Mechanosynthesis A THEORETICAL 1 Design and simulation of DMS tooltips a Need. Java applets, free software, interactive chemistry software, molecular modeling software. MDWeb is a personal workspace providing standard protocols to prepare structures, run standard molecular dynamics simulations and to analyze trajectories. DLPOLY is a general purpose classical molecular dynamics MD simulation software developed at Daresbury Laboratory by I. T. Todorov and W. Smith. MolviZ. Org. Molecular Visualization Resources all free and open source, collected by Eric Martz, including all Martzauthored molecular visualization. Molecular Workbench provides visual, interactive computational experiments for teaching and learning science. ELSEVIER VMD Visual Molecular Dynamics William Humphrey, Andrew Dalke, and Klaus Schulten Theoretical Biophysics Group, University of Illinois and Beckman. Automated Topology Builder ATBYes. Yes. Yes. No. No. No. No. No. No. Automated molecular topology building service for small molecules lt 9. 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. INo. No. Molecule building, editing peptides, small molecules, crystals, conformational analysis, 2. D3. D conversion extensible interfaces to other tools. Free open source. GNU GPLAvogadro. BOSSNo. No. Yes. No. Yes. No. Yes. No. No. OPLSProprietary. Yale University. CHARMMNo. Yes. Yes. Yes. Yes. IIYes. Yes. Commercial version with multiple graphical front ends is sold by Accelrys as CHARMmProprietary, commercialcharmm. CHEMKINNo. No. No. No. No. No. No. No. No. Chemical reaction kinetics. Proprietary. CHEMKINCOSMOSYes. Yes. Yes. Yes. Yes. No. INo. No. Hybrid QM MM COSMOS NMR force field with fast semi empirical calculation of electrostatic andor NMR properties 3 D graphical molecule builder and viewer. Proprietary, commercial, free without GUICOSMOS Software. CP2. KNo. No. Yes. Yes. Yes. No. Yes. Yes. Yes. CP2. K can perform atomistic and molecular simulations of solid state, liquid and biological systems. Free open source. GNU GPLv. 2 or later. CP2. KCulgi. Yes. Yes. Yes. Yes. Yes. No. INo. No. Atomistic simulations and mesoscale methods, database integration, mapping techniques, interface to MOPACNWChem. Proprietary. Culgi BVDesmond. 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. Schrdinger. 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. DLPOLYDLPOLY 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 ENCADNo. No. No. Yes. No. No. No. No. No. Notably the first MD simulation software by Michael Levitt. Free open source1fold. Y IYes. Yes. Yes. Yes. Yes. INo. No. University of Washington and The Baker Labs structure prediction, protein folding. Proprietary, commercial or gratisfold. Fold. XIYes. Yes. No. No. No. No. No. No. Energy calculations, protein design. Proprietary, commercial or gratis. CRGGPIUTMDIIYes. Yes. No. INo. No. Yes. Performs general purpose particle dynamics simulations on a single workstation, exploiting NVIDIA CUDA GPUs. Proprietaryhttp gpiutmd. GROMACSNo. No. No. Yes. No. Yes. IYes4Yes. High performance MDFree open source. GNU GPLgromacs. org. GROMOSNo. No. Yes. Yes. Yes. Yes. No. Yes. Yes. Intended for biomolecules. Proprietary, commercial. GROMOS website. GULPNo. No. Yes. Yes. No. Virtual Sailor 7 Serial Keygen Nero. No. No. No. No. Molecular dynamics and lattice optimization. Proprietary, free academic usehttps web. 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 sourcehttp glotzerlab. ICMYes. Yes. Yes. No. Yes. No. IYes. No. Powerful global optimizer in an arbitrary subset of internal variables, NOEs, docking protein, ligand, peptide, EM, density placement. Proprietary. Molsoft. LAMMPSYes. Yes. Yes. Yes. Yes. Yes. IYes. Yes. Has potentials for soft and solid state materials and coarse grain systems. Free open source, GNU GPLv. Sandia. Macro. Model. Yes. Yes. Yes. Yes. Yes. No. IYes. 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. Schrdinger. MAPSYes. 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. MBN Explorer5 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. Mede. AYes. 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 GPLTowhee Project. MDyna. Mix. No. No. No. Yes. No. No. No. No. No. Parallel MDFree open source. GNU GPLStockholm University. MOEYes. Yes. Yes. Yes. No. No. IYes. No. Molecular Operating Environment MOEProprietary. Chemical Computing Group. MOILYes. 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 codelink. Mol. Meccano. No. Yes. No. No. No. No. No. No. No. Semi automatic Force Field parametrizer. Proprietary. Mol. Meccano 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.