What is Molecular Modelling?
Molecular modeling
encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, drug design, computational biology and materials science for studying molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling techniques is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit (the Molecular mechanics approach), or explicitly modeling electrons of each atom (the quantum chemistry approach).
List of Free Softwares available
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.
encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, drug design, computational biology and materials science for studying molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling techniques is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit (the Molecular mechanics approach), or explicitly modeling electrons of each atom (the quantum chemistry approach).
List of Free Softwares available
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 | 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 | 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 | ||||
| Desmond | 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 | ||||
| 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 atIsfahan 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 | ? | High performance MD | Free | gromacs.org | ||||||
| GROMOS | 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 | 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, 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. | Not free | Schrödinger, LLC | ||
| 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, modifiedBeeman'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[4] | 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 | p4vasp.at | |||||||
| PyMol | Y | Y | Python-based viewer, many plugins to other software. Some mutagenisis. | Free, open source | PyMol.org | |||||||
| QMOL | Y | Protein viewer, provided byDNASTAR | Free | DNASTAR, Inc. | ||||||||
| RasMol | Y | Fast viewer | Free | RasMol | ||||||||
| Raster3D | Y | High quality raster images | Free | University of Washington | ||||||||
| RedMD[5] | 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 initiomodeling, 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, 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 performanceGPU-acceleratedab initio Molecular Dynamics and TD/DFT software package for very large molecular or even nanoscalesystems. The software runs onNVIDIA GPUs and64-bit Linux, and is based on heavily optimizedCUDA 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, MOPACand NAMDinterfaces, MD trajectory analysis, molecular docking, virtual screening, database engine, parallel design,OpenCLacceleration, 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 |
If you are a beginner in Molecular Modelling then here a book is for You to download free (OPEN access).
Molecular Modelling for Beginners, Second Edition
Publisher:JohnWiley & Sons Ltd 2008 | 411 Pages | ISBN: 9780470513132 | PDF | 12 MB
See the abstracts presented on Molecular modelling and docking studies in Chemistry in a Workshop held on Molecular modelling-2012---See here
In Next post, I try to evaluate all the softwares of Molecular modelling one by one and until then......Enjoy :)
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