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Modelling and Simulation
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
Abalone
Biomolecular simulations, protein folding. FreeACEMD
From Acellera Ltd, Molecular dynamics with CHARMM, Amber forcefields. Running on NVIDIA GPUs. Heavily optimized with CUDA. Basic version free. Commercial version available.Charmm, AMBER, user specified (through force field markup language, FFML), QM/MM calculations with Empirical Valence Bond (EVB); Framework based (GNUStep/cocoa); SCAAS for spherical boundary conditions
Free (licensed under GNU GPL)
AMBER[3]
Not freeambermd.org
Molecular building (DNA, proteins, hydrocarbons, nanotu
Molecular dynamics. GPU acceleration.
Free (GNU GPL) & CommercialADFQM
Ascalaph Project
Automated Topology Builder (ATB)
Automated molecular topology building service for small molecules (< 99 atoms). GROMOS, GROMACS, CNS formats with validation
Repository for molecular topologies and pre-equilibrated systems
Free for academic useAvogadro
Molecule building, editing (Peptides, small molecules, crystals), Conformational analysis, 2D/3D conversion. Extensible interfaces to other tools.
Free (GNU GPL)
BOSS
OPLS
Commercial
CHARMM
Commercial version with multiple graphical front ends is sold by Accelrys (as CHARMm)
Not freeCHEMKIN
Chemical reaction kintetics.
Not free
COSMOS
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.
Free(without GUI) and commercial< CP2K
CP2K can perform atomistic and molecular simulations of solid state, liquid and biological systems.
Free (GNU GPLv2 or later)< Culgi
Atomistic simulations and mesoscale methods.
Not free
Desmond
High Performance MD. Comes with a comprehensive GUI for building, visualizing, and reviewing results as well as calculation setup up and launching.
Free and commercial
Discovery Studio
Discovery Studio is a comprehensive life science modeling and simulation suite of applications focused on optimizing the drug discovery process. Capabilities include, small molecule simulations, QM/MM, pharmacophore modeling, QSAR, protein-ligand docking, protein homology modeling, sequence analysis, protein-protein docking, antibody modeling, etc.
Closed source/Trial available
fold.it
University of Washington and The Baker Labs. Structure prediction. Protein folding.
Free, download< FoldX
Energy calculations and protein design
Free for academic use
GPIUTMD
performs general purpose particle dynamics simulations on a single workstation, taking the advantage of NVIDIA CUDA GPUs.
Closed Source
GROMACS
High performance MD
Free (GNU GPLv2)
GROMOS
Geared towards biomolecules
Not free
GULP
Molecular dynamics and Lattice optimization
Free for academic use
HOOMD-blue
General-purpose Molecular Dynamics highly optimized for GPUs. Includes various pair potentials, Brownian dynamics, dissipative particle dynamics, rigid body constraints, energy minimization, etc…
Free, open source< ICM
Powerful global optimizer in an arbitrary subset of internal variables, NOEs, Protein docking, Ligand docking, Peptide docking, EM, Density placement
Not free< LAMMPS
Has potentials for soft and solid-state materials and coarse-grain systems
Free, Open Source. (GNU GPLv2)< MacroModel
OPLS-AA, MMFF, GBSA solvent model, conformational sampling, minimization, MD. Includes the Maestro GUI which provides visualization, molecule building, calculation setup, job launching and monitoring, project-level organization of results and access to a suite of other modelling programs.
Commercial< MAPS
Building, visualization and analysis tools in a single user interface together with access to multiple simulation engines.
Closed source/Trial available< Materials Studio
Materials Studio is a software environment that brings the materials simulation technology to desktop computing, solving key problems throughout the R&D process.
Closed source/Trial available< MCCCS Towhee
Originally designed for the prediction of fluid phase equilibria
Free< MDynaMix
Parallel MD
Free< MedeA
MedeA combines leading experimental databases and major computational programs like the Vienna Ab-Initio Simulation Package (VASP), LAMMPS, GIBBS with sophisticated materials property prediction, analysis, and visualization.
Closed source/Trial available< MOE
Molecular Operating Environment
Commercial< MOIL
Also includes action-based algorithms (Stochastic Difference Equation in Time and Stochastic Difference Equation in Length) and locally enhanced sampling.
Free< NAB[5]
Generation of Models for “Unusual” DNA and RNA
Free< NAMD + VMD
Fast, parallel MD, CUDA
Open source, free to academics< NWChem
High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM/MM methods
Open-source, Educational Community License version 2.0< ORAC
A Molecular Dynamics Simulation Program to Explore Free Energy Surfaces in Biomolecular Systems at the Atomistic Level
Free, open source< Packmol
Builds complex initial configurations for Molecular Dynamics
Free, Open Source. (GNU GPL)< Prime
Homology modeling, loop and side chain optimization, minimization, OPLS-AA, SGB solvent model, parallalized
Commercial< Protein Local Optimization Program
Helix, loop, and side chain optimization. Fast energy minimization.
Not free< 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.
Uppsala Molekylmekaniska HB< RedMD[6]
Reduced MD. Package for coarse-grained simulations.
Free on GNU Licence< 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)
Commercial< Spartan
Small molecule (< 2000 a.m.u.) MM and QM tools for determining conformation, structure, property, spectra, reactivity, and selectivity.
Commercial, Trial Available< StruMM3D (STR3DI32)
Sophisticated 3-D molecule builder and viewer, advanced structural analytical algorithms, full featured molecular modeling and quantitation of stereo-electronic effects, docking and the handling of complexes.
The 200 atom version is free< TeraChem
High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. The software runs on NVIDIA GPUs and 64-bit Linux, and is based on heavily optimized CUDA code.
Closed source / Trial licenses available< TINKER
Software tools for molecular design
Free< Tremolo-X
Fast, parallel MD
Not Free< UCSF Chimera
Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development.
University of California
VEGA ZZ
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.
Free for academic use
VEGA ZZ Web site
VLifeMDS
Complete Molecular Modelling Software, QSAR, Combinetorial Library generation, Pharmacophore, Cheminformatics, docking, etc.
Not free
Vlife Sciences Technologies
WHAT IF
Visualizer for MD. Interface to GROMACS.
Not free
WHAT IFYASARA Molecular-graphics, -modeling and -simulation program
Not free
YASARA.orgCambridge Structural Database (CSD) DB
Chem-X MP, DD, P xxx
ChemDBS-3D DD, DB xxx
CONCORD MB xxx
DGII MB xxx
GEMM G, BP xxx
GERM DD xxx
HONDO QM xxx
PQS: Parallel Quantum Solutions QM,MM
Profix BI
Protein Data Bank (PDB) DB, BP
Setor G xxx
Visual Molecular Dynamics (VMD) – 32 and 64 bit versions available G, MD
ZINDO QM xxx
Modelling and Simulation