Software for molecular mechanics modeling

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== Short list of molecular mechanics programs ==
== Short list of molecular mechanics programs ==
   
   
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<br />
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{| border="1;width:100%; height:300px;style=text-align:center"
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'''Min''' - Optimization,
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|+'''Table I:'''
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'''MD''' - Molecular Dynamics,
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'''MC''' - Monte Carlo,
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'''QM''' - Quantum mechanics.
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'''HA''' - Hardware accelerated.<br /><br />
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'''Y''' - Yes. <br />
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'''I''' - Has interface.
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{| class="wikitable"
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|-
|-
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!
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! style="background:green; color:white" |Software
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! View
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! style="background:green; color:white" |View 3D
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3D
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! style="background:green; color:white" |Model Builder  
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! Model
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! style="background:green; color:white" |Min - Optimization
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Builder
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! style="background:green; color:white" |Molecular Dynamics
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! Min
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! style="background:green; color:white" |Monte Carlo
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! MD
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! style="background:green; color:white" |Quantum mechanics
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! MC
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! style="background:green; color:white" |Hardware accelerated
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! QM
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! style="background:green; color:white" |Comments
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! HA
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! style="background:green; color:white" |License
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! Comments
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! License
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|-
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| [http://www.agilemolecule.com/AGM_Build.html AGM Build]
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!align:center| [http://www.agilemolecule.com/AGM_Build.html AGM Build]
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| '''Y'''
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!align:center|'''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| Model building with charges and MM atom types
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!align:center| Model building with charges and MM atom types
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| [[Free software|Free]] ([[GPL]])
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!align:center| [[Free software|Free]] ([[GPL]])
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| [[AMBER]]
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!align:center| [[AMBER]]
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| [http://www.agilemolecule.com/Ascalaph/Packages.html  Ascalaph]
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!align:center| [http://www.agilemolecule.com/Ascalaph/Packages.html  Ascalaph]
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''I'''
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!align:center| '''I'''
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| '''Y'''
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!align:center| '''Y'''
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| Molecular building (DNA, proteins, hydrocarbons, nanotubes).<br /> Molecular dynamics. GPU acceleration.
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!align:center| Molecular building (DNA, proteins, hydrocarbons, nanotubes).<br /> Molecular dynamics. GPU acceleration.
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| [http://zarbi.chem.yale.edu/software.html#boss BOSS]
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!align:center| [http://zarbi.chem.yale.edu/software.html#boss BOSS]
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| OPLS
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!align:center| OPLS
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| [[CHARMM]]
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!align:center| [[CHARMM]]
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''I'''
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!align:center| '''I'''
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| [http://www.acdlabs.com/products/chem_dsn_lab/chemsketch/ ChemSketch]
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!align:center| [http://www.acdlabs.com/products/chem_dsn_lab/chemsketch/ ChemSketch]
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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|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
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!align:center|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
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| [[GROMACS]]
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!align:center| [[GROMACS]]
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| '''Y'''
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!align:center| '''Y'''
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| '''?'''
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!align:center| '''?'''
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| High performance MD
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!align:center| High performance MD
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| [[GROMOS]]
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!align:center| [[GROMOS]]
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|'''Y'''
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!align:center|'''Y'''
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| '''Y'''
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!align:center| '''Y'''
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|Geared towards biomolecules
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!align:center|Geared towards biomolecules
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| [http://lammps.sandia.gov/ LAMMPS]
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!align:center| [http://lammps.sandia.gov/ LAMMPS]
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| '''Y'''
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!align:center| '''Y'''
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| Has potentials for soft and solid-state materials and coarse-grain systems
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!align:center| Has potentials for soft and solid-state materials and coarse-grain systems
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| [http://towhee.sourceforge.net/ MCCCS Towhee]
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!align:center| [http://towhee.sourceforge.net/ MCCCS Towhee]
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| '''Y'''
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!align:center| '''Y'''
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| Originally designed for the prediction of fluid phase equilibria
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!align:center| Originally designed for the prediction of fluid phase equilibria
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| [http://www.fos.su.se/~sasha/md_prog.html MDynaMix]
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!align:center| [http://www.fos.su.se/~sasha/md_prog.html MDynaMix]
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| '''Y'''
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!align:center| '''Y'''
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| Parallel MD
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!align:center| Parallel MD
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| [http://www.chemcomp.com/ MOE]
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!align:center| [http://www.chemcomp.com/ MOE]
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''I'''
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!align:center| '''I'''
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| Molecular Operating Environment
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!align:center| Molecular Operating Environment
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| [http://cbsu.tc.cornell.edu/software/moil/moil.html MOIL]
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!align:center| [http://cbsu.tc.cornell.edu/software/moil/moil.html MOIL]
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| Also includes action-based algorithms (Stochastic Difference Equation in Time and Stochastic Difference Equation in Length) and locally enhanced sampling.
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!align:center| Also includes action-based algorithms (Stochastic Difference Equation in Time and Stochastic Difference Equation in Length) and locally enhanced sampling.
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| [http://www.earth.ox.ac.uk/~keithr/moldy.html MOLDY]
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!align:center| [http://www.earth.ox.ac.uk/~keithr/moldy.html MOLDY]
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| '''Y'''
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!align:center| '''Y'''
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| Parallel, only pair-potentials, [[Cell lists]], modified [[Beeman's algorithm]]
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!align:center| Parallel, only pair-potentials, [[Cell lists]], modified [[Beeman's algorithm]]
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| [http://www.scripps.edu/mb/case/ NAB]
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!align:center| [http://www.scripps.edu/mb/case/ NAB]
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| '''Y'''
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!align:center| '''Y'''
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| Generation of Models for "Unusual" DNA and RNA
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!align:center|Generation of Models for "Unusual" DNA and RNA
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| [http://www.ime.unicamp.br/~martinez/packmol Packmol]
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!align:center| [http://www.ime.unicamp.br/~martinez/packmol Packmol]
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| '''Y'''
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!align:center| '''Y'''
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| Builds complex initial configurations for Molecular Dynamics
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!align:center| Builds complex initial configurations for Molecular Dynamics
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| [http://jacobson.compbio.ucsf.edu/plop_manual/plop_overview.htm Protein Local Optimization Program]
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!align:center| [http://jacobson.compbio.ucsf.edu/plop_manual/plop_overview.htm Protein Local Optimization Program]
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| Helix, loop, and side chain optimization.  Fast energy minimization.
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!align:center| Helix, loop, and side chain optimization.  Fast energy minimization.
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| [http://www.dnastar.com/products/qmol/index.html QMOL]
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!align:center| [http://www.dnastar.com/products/qmol/index.html QMOL]
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| '''Y'''
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!align:center| '''Y'''
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| Protein viewer
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!align:center| Protein viewer
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| [http://www.bernstein-plus-sons.com/software/rasmol/ RasMol]
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!align:center| [http://www.bernstein-plus-sons.com/software/rasmol/ RasMol]
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| '''Y'''
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!align:center| '''Y'''
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| Fast viewer
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!align:center| Fast viewer
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| [http://skuld.bmsc.washington.edu/raster3d/raster3d.html Raster3D]
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!align:center| [http://skuld.bmsc.washington.edu/raster3d/raster3d.html Raster3D]
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| '''Y'''
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!align:center| '''Y'''
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| High quality raster images
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!align:center| High quality raster images
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| [http://www.www.exorga.com/ STR3DI32]
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!align:center| [http://www.www.exorga.com/ STR3DI32]
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| Software for molecular design, bio-molecular simulations, docking of ligands, studying host-guest complexes
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!align:center| Software for molecular design, bio-molecular simulations, docking of ligands, studying host-guest complexes
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| [[TINKER]]
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!align:center| [[TINKER]]
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| '''I'''
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!align:center| '''I'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''I'''
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!align:center| '''I'''
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| Software Tools for Molecular Design
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!align:center| Software Tools for Molecular Design
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| [[UCSF_Chimera]]
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!align:center| [[UCSF_Chimera]]
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| '''Y'''
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!align:center| '''Y'''
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| Visually appealing viewer
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!align:center| Visually appealing viewer
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| [http://www.ks.uiuc.edu/Research/vmd/ VMD + NAMD]
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!align:center| [http://www.ks.uiuc.edu/Research/vmd/ VMD + NAMD]
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''?'''
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!align:center| '''?'''
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| Fast, parallel MD
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!align:center| Fast, parallel MD
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| [http://swift.cmbi.ru.nl/whatif/ WHAT IF]
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!align:center| [http://swift.cmbi.ru.nl/whatif/ WHAT IF]
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| '''Y'''
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!align:center| '''Y'''
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!align:center| '''Y'''
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| '''I'''
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!align:center| '''I'''
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| '''I'''
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!align:center| '''I'''
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| '''I'''
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!align:center| '''I'''
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| Visualizer for MD. Interface to GROMACS.
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!align:center|Visualizer for MD. Interface to GROMACS.
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| [http://sourceforge.net/projects/xeo  xeo]
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!align:center| [http://sourceforge.net/projects/xeo  xeo]
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| '''Y'''
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!align:center| '''Y'''
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!align:center| '''Y'''
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| open project management for nanostructures
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!align:center| open project management for nanostructures
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| [http://www.yasara.com/ YASARA]
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!align:center| [http://www.yasara.com/ YASARA]
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| Molecular-graphics, -modeling and -simulation program
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!align:center| Molecular-graphics, -modeling and -simulation program
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| [http://www.zeden.org/ Zodiac]
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!align:center| [http://www.zeden.org/ Zodiac]
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| '''Y'''
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!align:center| '''Y'''
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| Drug design suite
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!align:center| Drug design suite
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Current revision

[edit] Short list of molecular mechanics programs

Table I:
Software View 3D Model Builder Min - Optimization Molecular Dynamics Monte Carlo Quantum mechanics Hardware accelerated Comments License
AGM Build Y Y Model building with charges and MM atom types Free (GPL)
AMBER Y Y Y
Ascalaph Y Y Y I Y Molecular building (DNA, proteins, hydrocarbons, nanotubes).
Molecular dynamics. GPU acceleration.
BOSS Y Y Y OPLS
CHARMM Y Y Y Y I
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
GROMACS Y ? High performance MD
GROMOS Y Y Geared towards biomolecules
LAMMPS Y Has potentials for soft and solid-state materials and coarse-grain systems
MCCCS Towhee Y Originally designed for the prediction of fluid phase equilibria
MDynaMix Y Parallel MD
MOE Y Y Y Y I Molecular Operating Environment
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.
MOLDY Y Parallel, only pair-potentials, Cell lists, modified Beeman's algorithm
NAB Y Generation of Models for "Unusual" DNA and RNA
Packmol Y Builds complex initial configurations for Molecular Dynamics
Protein Local Optimization Program Y Y Y Y Helix, loop, and side chain optimization. Fast energy minimization.
QMOL Y Protein viewer
RasMol Y Fast viewer
Raster3D Y High quality raster images
STR3DI32 Y Y Y Y Software for molecular design, bio-molecular simulations, docking of ligands, studying host-guest complexes
TINKER I Y Y Y Y I Software Tools for Molecular Design
UCSF_Chimera Y Visually appealing viewer
VMD + NAMD Y Y Y Y ? Fast, parallel MD
WHAT IF Y Y I I I Visualizer for MD. Interface to GROMACS.
xeo Y Y open project management for nanostructures
YASARA Y Y Y Y Molecular-graphics, -modeling and -simulation program
Zodiac Y Y Y Drug design suite

[edit] See also

Quantum chemistry computer programs

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