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List of software for molecular mechanics modeling


List of software for molecular mechanics modeling

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
ACEMD[1] Y 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 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)
AMBER[3] Y Y Y Y I Y Y Not free
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
BOSS Y Y Y OPLS Commercial Yale University
CHARMM Y Y Y Y I I Y Y Commercial version with multiple graphical front ends is sold by Accelrys (as CHARMm) Not free
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
CP2K Y Y Y Y Y Y CP2K can perform atomistic and molecular simulations of solid state, liquid and biological systems. Free (GNU GPLv2 or later) CP2K
Culgi Y Y Y Y Y Atomistic simulations and mesoscale methods. Not free Culgi BV
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 Y / I Y Y Y Y Y I University of Washington and The Baker Labs. Structure prediction. Protein folding. Free, download download page
FoldX I Y Y Energy calculations and protein design Free for academic use CRG
GPIUTMD I I Y Y I Y performs general purpose particle dynamics simulations on a single workstation, taking the advantage of NVIDIA CUDA GPUs. Closed Source
GROMACS Y Y I Y[4] Y High performance MD Free (GNU GPLv2)
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
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
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
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
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
NAB[5] Y Generation of Models for "Unusual" DNA and RNA Free Case group
NAMD + VMD Y Y Y Y Y Y Y Fast, parallel MD, CUDA Open source, free to academics Beckman Institute
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 Free, Open Source. (GNU GPL) 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
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
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.
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
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.
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
WHAT IF Y Y I I I Visualizer for MD. Interface to GROMACS. Not free WHAT IF
YASARA Y Y Y Y Y Molecular-graphics, -modeling and -simulation program Not free

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.  
  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.  
  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.  
  4. ^
  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.  

External links

  • Linux4Chemistry
  • Collaborative Computational Project
  • World Index of Molecular Visualization Resources
  • Short list of Molecular Modeling resources
  • OpenScience
  • Biological Magnetic Resonance Data Bank
  • Materials modelling and computer simulation codes
  • A few tips on molecular dynamics
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