Comparison of software for molecular mechanics modeling


This is a list of computer programs that are predominantly used for molecular mechanics calculations.
NameView 3DModel builderMinMDMCREMQMImpGPUCommentsLicenseWebsite
AbaloneBiomolecular simulations, protein folding., gratis, commercial
ADFModeling suite: ReaxFF, UFF, QM-MM with Amber and Tripos force fields, DFT and semi-empirical methods, conformational analysis with RDKit; partly GPU-accelerated, commercial, gratis trial
Ascalaph DesignerMolecular building, molecular dynamics, GPU acceleration
AvogadroMolecule building, editing, conformational analysis, 2D/3D conversion; extensible interfaces to other tools open source GNU GPL
BOSSOPLS
CHARMMCommercial version with multiple graphical front ends is sold by Accelrys , commercial
CHEMKINChemical reaction kinetics.
CP2KCP2K can perform atomistic and molecular simulations of solid state, liquid and biological systems. open source GNU GPLv2 or later
DesmondHigh performance MD; has comprehensive GUI to build, visualize, and review results and calculation setup up and launch, commercial or gratis
Discovery StudioComprehensive 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., trial available
fold.itY / IUniversity of Washington and The Baker Labs; structure prediction, protein folding, commercial or gratis
FoldXEnergy calculations, protein design, commercial or gratis
GROMACSHigh performance MD open source GNU GPL
GROMOSIntended for biomolecules, commercial
HyperChemMM+, Ambers, Amber2, Amber3, Amber94, Amber96, Amber99, Bio+83, Bio+85, Charmm-19, Charmm-22, Charmm-27, OPLS, Custom, Extended-Hukel, CNDO, INDO, MINDO3, MNDO, MNDO/d, AM1, PM3, RM1, ZINDO/1, ZINDO/s, TNDO, Hartreee-Fock, MP2, CI, Density Functional Theories, solvent model, conformational sampling, minimizing, MD, MC, Langevin. QM/MM calculations can be used. Includes the HyperChem 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. Developer's kit using HCL, C, C++, Visual Basic, Fortran, Tcl/Tk, DDE., trial available
LAMMPSHas potentials for soft and solid-state materials and coarse-grain systems open source, GNU GPLv2
MacroModelOPLS-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.
MAPSBuilding, visualizing, and analysis tools in one user interface, with access to multiple simulation engines, trial available
Materials StudioEnvironment that brings materials simulation technology to desktop computing, solving key problems in R&D processes, trial available
MBN Explorer + MBN StudioStandard and reactive CHARMM force fields; molecular modeler ; explicit library of examples, free trial available
MDynaMixParallel MD open source GNU GPL
MOE
OracMolecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level open source
NAMD + VMDFast, parallel MD, CUDA, free academic use, source code
NWChemHigh-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM-MM methods open source, Educational Community License version 2.0
Protein Local Optimization ProgramHelix, loop, and side chain optimizing, fast energy minimizing
Q Free energy perturbation simulations, empirical valence bond, calculations of reaction free energies, linear interaction energy calculations of receptor-ligand binding affinities open source GNU GPLv2 or later
SAMSONComputational nanoscience. Modular architecture, modules termed SAMSON Elements, gratis
ScigressMM, DFT, semiempirical methods, parallel MD, conformational analysis, Linear scaling SCF, docking protein-ligand, Batch processing, virtual screening, automated builders
SpartanSmall molecule MM and QM tools to determine conformation, structure, property, spectra, reactivity, and selectivity., free trial available
TeraChemHigh 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., trial licenses available
TINKERSoftware tools for molecular design-Tinker-OpenMM
Software tools for molecular design-Tinker-HP		, gratis
Tremolo-XFast, parallel MD
UCSF ChimeraVisually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development., free academic use
YASARAMolecular graphics, modeling, simulation