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Comparison 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, HA - Hardware accelerated.

Y - Yes.
I - Has interface.

Name View

3D

Model

Builder

Min MD MC REM QM Imp HA Comments License Website
Abalone Y Y Y Y Y Y I Y Y Biomolecular simulations, protein folding. Free Agile Molecule
ACEMD[1] 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
ADUN[2] 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 adun.imim.es
AMBER[3] Y Y Y Y Y Not free ambermd.org
Ascalaph Designer Y Y Y Y I Y Y Molecular building (DNA, proteins, hydrocarbons, nanotubes).
Molecular dynamics. GPU acceleration. 		Free & Commercial Ascalaph Project
Automated Topology Builder (ATB) 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, open source Avogadro
Balloon Y Y 2D/3D conversion and conformational analysis. Free to use, 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 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 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
Desmond Y Y Y High Performance MD. Free and commercial D. E. Shaw Research
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
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
GROMACS Y Y ? High performance MD Free gromacs.org
GROMOS Y Y Geared towards biomolecules Not free GROMOS Homepage
ICM Y Y Y Y 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 I Y Has potentials for soft and solid-state materials and coarse-grain systems Free Sandia
MacroModel Y Y Y Y Y I Y OPLS-AA, GBSA solvent model, conformational sampling, minimization, MD Not free Schrödinger, LLC
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) with sophisticated materials property prediction, analysis, and visualization. Closed source/Not free link
MCCCS Towhee Y Originally designed for the prediction of fluid phase equilibria Free Towhee Project
MDynaMix[4] 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 A Molecular Dynamics Simulation Program to Explore Free Energy Surfaces in Biomolecular Systems at the Atomistic Level Free, open source ORAC download page
NAB[5] Y Generation of Models for "Unusual" DNA and RNA Free Case group
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 link
Protein Local Optimization Program Y Y Y Y Helix, loop, and side chain optimization. Fast energy minimization. Not free link
p4vasp Y Y Python-based viewer, structure builder and VASP results browser. Shows band-structure, charge densities and simulates STM images. Free, open source Download at [1], Original web [2]
PyMol Y Y Python-based viewer, many plugins to other software. Some mutagenisis. Free, open source [3]
QMOL Y Protein viewer, provided by DNASTAR Free DNASTAR, Inc.
RasMol Y Fast viewer Free RasMol
Raster3D Y High quality raster images Free University of Washington
RedMD[6] 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
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, specra, 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 [7] 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. Unpublished source / Trial licenses available TeraChem
TINKER I Y Y Y Y I Y Software tools for molecular design Free Washington University
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
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 Fast, parallel MD Free 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 Molecular-graphics, -modeling and -simulation program Not free YASARA.org
Zodiac Y Y Y Drug design suite link

See also

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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  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: 5179–5197. doi:10.1021/ja00124a002.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ Lyubartsev AP, Laaksonen A (2000). "MDynaMix - A scalable portable parallel MD simulation package for arbitrary molecular mixtures". Computer Physics Communications. 128: 565–589. doi:10.1016/S0010-4655(99)00529-9.
  5. ^ Macke T, Case DA (1998). "Modeling unusual nucleic acid structures". Molecular Modeling of Nucleic Acids: 379–393.
  6. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  7. ^ JCTC citation needed.
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