Comparison of software for molecular mechanics modeling

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

Name View 3D Model builder Min MD MC REM QM Imp GPU Comments License Website AMBERHigh Performance MD, Comprehensive analysis toolsProprietary, Free open sourceAMBER MD Abalone Biomolecular simulations, protein folding. , gratis, commercial Agile Molecule ADF Modeling 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 SCM Ascalaph Designer Molecular building (DNA, proteins, hydrocarbons, nanotubes), molecular dynamics, GPU acceleration Ascalaph Project Avogadro Molecule building, editing (peptides, small molecules, crystals), conformational analysis, 2D/3D conversion; extensible interfaces to other tools open source GNU GPL Avogadro BOSS OPLS Yale University CHARMM Commercial version with multiple graphical front ends is sold by BIOVIA (as CHARMm), formerly Accelrys. , commercial charmm.org CHEMKIN Chemical reaction kinetics. CHEMKIN CP2K CP2K can perform atomistic and molecular simulations of solid state, liquid and biological systems. open source GNU GPLv2 or later CP2K Desmond High performance MD; has comprehensive GUI to build, visualize, and review results and calculation setup up and launch , commercial or gratis D. E. Shaw Research Schrödinger Discovery Studio 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. , trial available Dassault Systèmes BIOVIA(formerly Accelrys)DL_POLYYesYesYesYesNoNoNoNoNoGeneral-purpose parallel classical molecular dynamics package with energy-minimization methods and a Java GUI for visualization and model preparation.Free and open-source, LGPLv3DL_POLY fold.it Y / I University of Washington and The Baker Labs; structure prediction, protein folding , commercial or gratis fold.it download page FoldX Energy calculations, protein design , commercial or gratis CRG GROMACS Implicit Solvent – Gromacs High performance MD open source GNU GPL gromacs.org GROMOS Intended for biomolecules , commercial GROMOS website LAMMPS Has potentials for soft and solid-state materials and coarse-grain systems open source, GNU GPLv2 Sandia MacroModel 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. Schrödinger Materials Studio Environment that brings materials simulation technology to desktop computing, solving key problems in R&D processes , trial available Dassault Systèmes BIOVIA(formerly Accelrys) MBN Explorer + MBN Studio Standard and reactive CHARMM force fields; molecular modeler (carbon nanomaterials, biomolecules, nanocrystals); explicit library of examples , free trial available MBN Research Center MDynaMix Parallel MD open source GNU GPL Stockholm University MOE Molecular Operating Environment (MOE) Chemical Computing Group ms2 direct on the fly computation of large number of thermophysical properties. Main application of ms2 is on fluids. open sourcems-2.de OpenMMHigh Performance MD, highly flexible, Python scriptable open source MITOpenMM Orac Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level open source Orac download page NAMD + VMD Fast, parallel MD, CUDA , free academic use, source code Beckman Institute NWChem High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM-MM methods open source, Educational Community License version 2.0 NWChem Protein Local Optimization Program Helix, loop, and side chain optimizing, fast energy minimizing PLOP wiki Q (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 open source GNU GPLv2 or later Q QuantumATK Complete atomistic modeling platform for material science. It includes DFT (Plane-Wave and LCAO), Semi-empirical, and Force Field simulation engines. , commercial Synopsys QuantumATK Quantum ESPRESSO Open-source suite focused on electronic-structure calculations and MD (particularly CPMD), popular for its flexibility and extensive community support. open source GNU GPLv2 or later Quantum ESPRESSO SAMSON Computational nanoscience (life sciences, materials, etc.). Modular architecture, modules termed SAMSON Elements , gratis SAMSON Connect Scigress MM, DFT, semiempirical methods, parallel MD, conformational analysis, Linear scaling SCF, docking protein-ligand, Batch processing, virtual screening, automated builders (molecular dynamics, proteins, crystals) SCIGRESS.com Spartan Small molecule (< 2,000 a.m.u.) MM and QM tools to determine conformation, structure, property, spectra, reactivity, and selectivity. , free trial available Wavefunction, Inc. TeraChem 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. , trial licenses available PetaChem LLC TINKER Software tools for molecular design-Tinker-OpenMM Software tools for molecular design-Tinker-HP , gratis Washington University UCSF Chimera Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development. , free academic use University of California VASP Highly efficient DFT code often used in materials science providing excellent performance on large systems. VASP YASARA Molecular graphics, modeling, simulation YASARA.org

Comparison of software for molecular mechanics modeling

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