List of software for molecular mechanics modeling

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

Min - Optimization, MD - Molecular Dynamics, MC - Monte Carlo, REM - Replica exchange method, QM - Quantum mechanics, Imp - Implicit water, GPU - GPU accelerated.

Y - Yes.
I - Has interface.

Name View

3D

Model

Builder

Min MD MC REM QM Imp GPU Comments License Website
Abalone Y Y Y Y Y Y I Y Y Biomolecular simulations, protein folding. Free Agile Molecule
ACEMD1 Y Y Y Molecular dynamics with CHARMM, Amber forcefields. Running on NVIDIA GPUs. Heavily optimized with CUDA. Basic version free. Commercial version available. Acellera Ltd
ADUN2 Y Y Y Y Y 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) adun.imim.es
AMBER3 Y Y Y Y Y Y Not free ambermd.org
Ascalaph Designer Y Y Y Y Y Y I Y Y Molecular building (DNA, proteins, hydrocarbons, nanotubes).
Molecular dynamics. GPU acceleration.
Free (GNU GPL) & Commercial Ascalaph Project
Automated Topology Builder (ATB) Y Y Y 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 use Automated Topology Builder
Avogadro Y Y Y I Molecule building, editing (Peptides, small molecules, crystals), Conformational analysis, 2D/3D conversion. Extensible interfaces to other tools. Free (GNU GPL) Avogadro
Balloon Y Y 2D/3D conversion and conformational analysis. Usage free, closed source Åbo Akademi
BOSS Y Y Y OPLS Commercial Yale University
CHARMM Y Y Y Y I I Y Commercial version with multiple graphical front ends is sold by Accelrys (as CHARMm) Not free charmm.org
Chemitorium Y Y Free 2D/3D graphical organic molecule builder, viewer and visualisation tool. Free (GNU GPL) link
ChemSketch Y Y Y Fast 2-D graphical molecule builder and 3-D viewer. Contains simplified CHARMM for fast stable inaccurate optimization of single molecules up to 1000 atoms Free Advanced Chemistry Development, Inc.
COSMOS Y Y Y Y Y I 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 COSMOS Software
Culgi Y Y Y Y Y Atomistic simulations and mesoscale methods. Not free Culgi BV
Deneb Y Y I I I Deneb is a powerful application capable of managing hundreds of projects, each containing hundreds of simulations applied to different samples,every one containing thousands of atoms.

Deneb interfaces with most relevant simulation packages (SIESTA, QE, VASP,etc.): Launch your simulation into a remote host with a single click, Deneb will monitor them for you and retrieve the outputs.

Commercial/Trial available AtelGraphics inc.
Desmond Y Y Y Y Y Y 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 D. E. Shaw Research Schrödinger
Discovery Studio Y Y Y Y Y Y Y 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 Accelrys
fold.it Y / I Y Y Y Y Y I University of Washington and The Baker Labs. Structure prediction. Protein folding. Free, download fold.it download page
FoldX I Y Y Energy calculations and protein design Free for academic use CRG
GoVASP Y I I I GoVASP is a sophisticated graphical user interface for the Vienna Ab-Initio Simulation Package (VASP). GoVASP comprises tools to prepare, perform and monitor VASP calculations and to evaluate and visualize the computed data. Closed source/Not free/Trial available Windiks Consulting
GPIUTMD I I Y Y I Y GPIUTMD stands for Graphic Processors at Isfahan University of Technology for Many-particle Dynamics. It performs general purpose particle dynamics simulations on a single workstation, taking the advantage of NVIDIA CUDA GPUs to attain a level of performance equivalent to hundreds of processors on a fast cluster. Closed source/Not free/Demo available GPIUTMD
GROMACS Y Y Y High performance MD Free (GNU GPLv2) gromacs.org
GROMOS Y Y Y Y Y Y Geared towards biomolecules Not free GROMOS Homepage
GULP Y Y Molecular dynamics and Lattice optimization Free for academic use https://projects.ivec.org/gulp/
HOOMD-blue Y Y Y 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 http://codeblue.umich.edu/hoomd-blue/index.html
ICM Y Y Y Y I Y Powerful global optimizer in an arbitrary subset of internal variables, NOEs, Protein docking, Ligand docking, Peptide docking, EM, Density placement Not free Molsoft
LAMMPS Y Y Y Y I Y Has potentials for soft and solid-state materials and coarse-grain systems Free, Open Source. (GNU GPLv2) Sandia
Lasergene Structural Biology Suite Y Y DNASTAR's Lasergene Structural Biology Suite provides structural biologists a set of tools for protein sequence analysis, macromolecular visualization, and structure prediction. It includes Protean 3D, an application for exploring macromolecular structure, motion, and function, and NovaFold, an application for predicting three-dimensional structures for protein sequences. Commercial/Trial available DNASTAR, Inc.
LPMD Y Y Y Y Common neighbor analysis (CNA) to detect structures (BCC, FCC, HCP, SC), Radial Distribution Function (pair correlation function, g(r)), Mean Squared Displacement (MSD), Velocity Autocorrelation function (vacf), Angle Distribution function, Density profile of the sample, Temperature profile of the sample, Pairs distances, Convert between formats (VASP, DLPOLY, XYZ, PDB...), Reads/Writes multiple formats, Makes animations and pictures, Complex Simulation Cells builder (create planes, spheres, cylinders, boxes, etc.). Free, Open Source. (GNU GPLv2) [www.lpmd.cl]
MacroModel Y Y Y Y Y I Y 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 Schrödinger
MAPS Y Y Y Y Y Y Y Building, visualization and analysis tools in a single user interface together with access to multiple simulation engines. Closed source/Trial available Scienomics
Materials Studio Y Y Y Y Y Y Y Y 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 Accelrys
MedeA Y Y Y Y Y Y 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 Materials Design
MCCCS Towhee Y Originally designed for the prediction of fluid phase equilibria Free Towhee Project
MDynaMix Y Parallel MD Free Stockholm University
MOE Y Y Y Y I Y Molecular Operating Environment Commercial Chemical Computing Group
MOIL Y Y Y Y Also includes action-based algorithms (Stochastic Difference Equation in Time and Stochastic Difference Equation in Length) and locally enhanced sampling. Free link
molecools Y Y Simple Javascript molecular visualization tool link
MOLDY Y Parallel, only pair-potentials, Cell lists, modified Beeman's algorithm Free Moldy
ORAC Y Y Y Y A Molecular Dynamics Simulation Program to Explore Free Energy Surfaces in Biomolecular Systems at the Atomistic Level Free, open source ORAC download page
NAB4 Y Generation of Models for "Unusual" DNA and RNA Free Case group
NWChem Y Y Y High-performance computational chemistry software, includes quantum mechanics, molecular dynamics and combined QM/MM methods Open-source, Educational Community License version 2.0 NWChem
Packmol Y Builds complex initial configurations for Molecular Dynamics link
Prime Y Y Y Y I Y Homology modeling, loop and side chain optimization, minimization, OPLS-AA, SGB solvent model, parallalized Commercial Schrödinger
Protein Local Optimization Program Y Y Y Y Helix, loop, and side chain optimization. Fast energy minimization. Not free PLOP wiki
p4vasp Y Y Python-based viewer, structure builder and VASP results browser. Shows band-structure, charge densities and simulates STM images. Free, open source p4vasp.at
PyMOL Y Y Python-based viewer, many plugins to other software. Some mutagenisis. Free, open source PyMol.org
Q Y (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 Q
RasMol Y Fast viewer Free RasMol
Raster3D Y High quality raster images Free University of Washington
RedMD5 I Y Y Y Y Reduced MD. Package for coarse-grained simulations. Free on GNU Licence University of Warsaw, ICM
StruMM3D (STR3DI32) Y Y Y Y ' ' 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 Exorga, Inc.
Selvita Protein Modeling Platform Y Y Y Y Protein structure prediction, homology modeling, ab initio modeling, loop modeling, protein threading Commercial Selvita Ltd
SCIGRESS Y Y Y Y Y Y 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 SCIGRESS.com
SimBioSys' MoDeST (Molecular Design Software Toolkit) Y Y Y Y molecular docking, scoring functions for docking, "ligand-based", "fragment-based", "de-novo" Not Free SimBioSys Inc.
Spartan Y Y Y Y Y Y Small molecule (< 2000 a.m.u.) MM and QM tools for determining conformation, structure, property, spectra, reactivity, and selectivity. Commercial, Trial Available Wavefunction, Inc.
SwissParam Web server to determine automatically parameters and topologies for small organic molecules, for use with the CHARMM all atoms force field. Files can be used with CHARMM and GROMACS. Free for academic. CHARMm licence required for commercial usage. SwissParam.
TeraChem Y Y Y Y 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 PetaChem LLC
TINKER I Y Y Y Y I Y Software tools for molecular design Free Washington University
Tremolo-X I Y Y Fast, parallel MD Not Free Tremolo-X
UCSF Chimera Y Y Y Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development. University of California
VEGA ZZ Y Y Y I Y Y Y 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 Y Y Y Y I Y Complete Molecular Modelling Software, QSAR, Combinetorial Library generation, Pharmacophore, Cheminformatics, docking, etc. Not free Vlife Sciences Technologies
VMD + NAMD Y Y Y Y Y Y Y Fast, parallel MD, CUDA Open source, free to academics Beckman Institute
WHAT IF Y Y I I I Visualizer for MD. Interface to GROMACS. Not free WHAT IF
xeo Y Y open project management for nanostructures link
YASARA Y Y Y Y Y Molecular-graphics, -modeling and -simulation program Not free YASARA.org
Zodiac Y Y Y Drug design suite link

See also

Notes and references

  1. ^ M. J. Harvey, G. Giupponi and G. De Fabritiis (2009). "ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale". Journal of Chemical Theory and Computation 5 (6): 1632–1639. doi:10.1021/ct9000685. 
  2. ^ Johnston, MA, Fernández-Galván, I, Villà-Freixa, J (2005). "Framework-based design of a new all-purpose molecular simulation application: the Adun simulator". J. Comp. Chem. 26 (15): 1647–1659. doi:10.1002/jcc.20312. PMID 16175583. 
  3. ^ Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995). "A second generation force field for the simulation of proteins, nucleic acids, and organic molecules". J. Am. Chem. Soc. 117 (19): 5179–5197. doi:10.1021/ja00124a002. 
  4. ^ Macke T, Case DA (1998). "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379–393. 
  5. ^ A. Górecki, M. Szypowski, M. Długosz and J. Trylska (2009). "RedMD - Reduced molecular dynamics package". J. Comp. Chem. 30 (14): 2364–2373. doi:10.1002/jcc.21223. PMID 19247989. 

External links








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