SklogWiki - User contributions [en]

BD BOX

2016-07-05T11:25:54Z

Mdlugosz:

'''BD_BOX''' is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms.
BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened electrostatics in dielectric media and Lennard-Jones functions. Hydrodynamically correlated motions of particles are modeled using configuration-dependent diffusion tensors. Brownian dynamics simulations can be performed either for single molecules or periodic multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields.
Starting with the version 2.1, one can also simulate with BD_BOX rigid bodies that are described with fully anisotropic diffusion tensors. Rigid molecules can be described either using a coarse-grained representation or at the atomistic level of detail. In the latter case, intermolecular interactions may include electrostatic, hydrophobic and Lennard-Jones potentials. External electric fields can also be applied to the simulated system.
BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.

Work on BD_BOX is supported by Polish National Science Centre.

==References==
[http://dx.doi.org/10.1002/jcc.21847 Długosz, M.; Zieliński, P.; Trylska, J. Brownian dynamics simulations on CPU and GPU with BD_BOX J. Comput. Chem., 32, 2734-2744, 2011]

[http://pubs.acs.org/doi/abs/10.1021/ct500124r Długosz, M.; Antosiewicz, J. Anisotropic diffusion effects on the barnase-barstar encounter kinetics J. Chem. Theory Comput., 9, 1667-1677, 2013]

[http://pubs.acs.org/doi/pdf/10.1021/ct300937z Długosz, M.; Antosiewicz, J. Transient effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules J. Chem. Theory Comput., 10, 2583-290, 2014]

[http://pubs.acs.org/doi/pdf/10.1021/ct4008519 Długosz, M.; Antosiewicz, J. Evaluation of proteins' rotational diffusion coefficients from simulations of their free Brownian motion in volume-occupied environments J. Chem. Theory Comput., 10, 481-491, 2014]

==External links==
*[http://www3.cent.uw.edu.pl/~mdlugosz/#download BD_BOX Home Page]

[[Category: Materials modelling and computer simulation codes]]

BD BOX

2016-07-05T11:24:10Z

Mdlugosz:

'''BD_BOX''' is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms.
BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened electrostatics in dielectric media and Lennard-Jones functions. Hydrodynamically correlated motions of particles are modeled using configuration-dependent diffusion tensors. Brownian dynamics simulations can be performed either for single molecules or periodic multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields.
Starting with the version 2.1, one can also simulate with BD_BOX rigid bodies that are described with fully anisotropic diffusion tensors. Rigid molecules can be described either using a coarse-grained representation or at the atomistic level of detail. In the latter case, intermolecular interactions may include electrostatic, hydrophobic and Lennard-Jones potentials. External electric fields can also be applied to the simulated system.
BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.

Work on BD_BOX is supported by Polish National Science Centre.

==References==
[http://dx.doi.org/10.1002/jcc.21847 Długosz, M.; Zieliński, P.; Trylska, J. Brownian dynamics simulations on CPU and GPU with BD_BOX J. Comput. Chem., 32, 2734-2744, 2011]

[http://pubs.acs.org/doi/abs/10.1021/ct500124r Długosz, M.; Antosiewicz, J. Anisotropic diffusion effects on the barnase-barstar encounter kinetics J. Chem. Theory Comput., 9, 1667-1677, 2013]

[http://pubs.acs.org/doi/pdf/10.1021/ct300937z Długosz, M.; Antosiewicz, J. Transient effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules J. Chem. Theory Comput., 10, 2583-290, 2014]

[http://pubs.acs.org/doi/pdf/10.1021/ct4008519 Długosz, M.; Antosiewicz, J. Evaluation of proteins' rotational diffusion coefficients from simulations of their free Brownian motion in volume-occupied environments J. Chem. Theory Comput., 10, 481-491, 2014]

==External links==
*[http://www3.cent.uw.edu.pl/~mdlugosz BD_BOX Home Page]

[[Category: Materials modelling and computer simulation codes]]

BD BOX

2014-10-21T11:58:22Z

Mdlugosz:

'''BD_BOX''' is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms.
BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened electrostatics in dielectric media and Lennard-Jones functions. Hydrodynamically correlated motions of particles are modeled using configuration-dependent diffusion tensors. Brownian dynamics simulations can be performed either for single molecules or periodic multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields.
Starting with the version 2.1, one can also simulate with BD_BOX rigid bodies that are described with fully anisotropic diffusion tensors. Rigid molecules can be described either using a coarse-grained representation or at the atomistic level of detail. In the latter case, intermolecular interactions may include electrostatic, hydrophobic and Lennard-Jones potentials. External electric fields can also be applied to the simulated system.
BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.

Work on BD_BOX is supported by Polish National Science Centre.

==References==
[http://dx.doi.org/10.1002/jcc.21847 Długosz, M.; Zieliński, P.; Trylska, J. Brownian dynamics simulations on CPU and GPU with BD_BOX J. Comput. Chem., 32, 2734-2744, 2011]

[http://pubs.acs.org/doi/abs/10.1021/ct500124r Długosz, M.; Antosiewicz, J. Anisotropic diffusion effects on the barnase-barstar encounter kinetics J. Chem. Theory Comput., 9, 1667-1677, 2013]

[http://pubs.acs.org/doi/pdf/10.1021/ct300937z Długosz, M.; Antosiewicz, J. Transient effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules J. Chem. Theory Comput., 10, 2583-290, 2014]

[http://pubs.acs.org/doi/pdf/10.1021/ct4008519 Długosz, M.; Antosiewicz, J. Evaluation of proteins' rotational diffusion coefficients from simulations of their free Brownian motion in volume-occupied environments J. Chem. Theory Comput., 10, 481-491, 2014]

==External links==
*[http://browniandynamics.org BD_BOX Home Page]

[[Category: Materials modelling and computer simulation codes]]

BD BOX

2014-10-21T11:52:55Z

Mdlugosz:

'''BD_BOX''' UNIQa0eb08b6ad1b2077-ref-00000006-QINU
is an open source, scalable [[Brownian dynamics]] package for UNIX/LINUX platforms.
BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened electrostatics in dielectric media and Lennard-Jones functions. Hydrodynamically correlated motions of particles are modeled using configuration-dependent diffusion tensors. Brownian dynamics simulations can be performed either for single molecules or periodic multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields.
Starting with the version 2.1, one can also simulate with BD_BOX rigid bodies that are described with fully anisotropic diffusion tensors. Rigid molecules can be described either using a coarse-grained representation or at the atomistic level of detail. In the latter case, intermolecular interactions may include electrostatic, hydrophobic and Lennard-Jones potentials. External electric fields can also be applied to the simulated system.
BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.

Work on BD_BOX is supported by Polish National Science Centre.

==References==
UNIQa0eb08b6ad1b2077-references-00000007-QINU
==External links==
*[http://browniandynamics.org BD_BOX Home Page]

[[Category: Materials modelling and computer simulation codes]]

BD BOX

2011-10-19T15:58:26Z

Mdlugosz:

'''BD_BOX''' program <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", J. Comput. Chem., 32:2734–2744, 2011</ref>

BD_BOX is an open source, scalable Brownian dynamics package for UNIX/LINUX platforms. BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened electrostatics in dielectric media and Lennard-Jones functions. Hydrodynamically correlated motions of particles are modeled using configuration-dependent diffusion tensors. Brownian dynamics simulations can be performed either for single molecules or periodic multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields. BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.

Work on BD_BOX is supported by Polish National Science Centre.

==References==
<references/>
==External links==
*[http://bionano.icm.edu.pl/software/bd_box BD_BOX Home Page]

[[Category: Materials modelling and computer simulation codes]]

BD BOX

2011-10-19T15:57:00Z

Mdlugosz:

'''BD_BOX''' program <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", J. Comput. Chem., 32:2734–2744, 2011</ref>

BD_BOX is an open source, scalable Brownian dynamics package for UNIX/LINUX platforms. BD_BOX uses flexible bead models to represent macromolecules. Molecules consist of spherical subunits connected with deformable bonds. Bonded interactions resulting in deformations of planar and dihedral angles can also be included. Nonbonded potentials include pairwise functions describing screened electrostatics in dielectric media and Lennard-Jones functions. Hydrodynamically correlated motions of particles are modeled using configuration-dependent diffusion tensors. Brownian dynamics simulations can be performed either for single molecules or periodic multimolecular systems. It is also possible to simulate systems influenced by external factors such as various electric fields. BD_BOX is written in C and uses modern computer architectures and technologies: MPI for distributed-memory platforms, OpenMP for shared-memory systems, SSE vectorization for CPU and NVIDIA CUDA framework for GPGPU.

Work on BD_BOX is supported by Polish National Science Centre.

==References==
<references/>
==External links==
*[http://http://bionano.icm.edu.pl/software/bd_box BD_BOX Home Page]

[[Category: Materials modelling and computer simulation codes]]

BD BOX

2011-10-19T15:56:15Z

Mdlugosz: Created page with "'''BD_BOX''' program <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", J. ..."

'''BD_BOX''' program <ref>[http://dx.doi.org/10.1002/jcc.21847 Maciej Długosz, Paweł Zieliński, Joanna Trylska, "Brownian dynamics simulations on CPU and GPU with BD_BOX", J. Comput. Chem., 32:2734–2744, 2011</ref>
==References==
<references/>
==External links==
*[http://http://bionano.icm.edu.pl/software/bd_box BD_BOX Home Page]

[[Category: Materials modelling and computer simulation codes]]

Materials modelling and computer simulation codes

2011-10-19T15:52:19Z

Mdlugosz:

The following is a sortable list (to change sort criteria click on the square icon next to the column title) of software for use in materials modelling and computer simulation. The use of simulation software whose source code you have access to (for example, Open Source, or GNU General Public License) is a fundamental tenet of good practice, and is highly recommended <ref>[http://dx.doi.org/10.1063/1.476021 Wilfred F. van Gunsteren, and Alan E. Mark "Validation of molecular dynamics simulation", Journal of Chemical Physics '''108''' pp. 6109-6116 (1998)]</ref>.
{| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0"
|-
! Computer program !! Focus !! class="unsortable" | Notes !! License
|-
|[[Abalone]]
|[[molecular dynamics]], visualisation
|biopolimers
|Free
|-
|[[ACEMD]]
|[[molecular dynamics]]
|biopolimers
|free/commercial
|-
|[[AMBER -- Assisted Model Building with Energy Refinement | AMBER]]
|[[molecular dynamics]]
|Assisted Model Building with Energy Refinement
|commercial
|-
|[[BD_BOX]]
|[[Brownian dynamics]]
|scalable (CPU/GPU) Brownian dynamics package for UNIX/LINUX platforms
|GNU Public License
|-
|[[BOSS]]
|
| '''B'''iochemical and '''O'''rganic '''S'''imulation '''S'''ystem
|commercial
|-
|[[BRAHMS]]
|[[molecular dynamics]]
|'''B'''iomembrane '''R'''educed-'''A'''pproac'''H''' '''M'''olecular '''S'''imulator
|in development
|-
|[[CASTEP]]
|[[density-functional theory]]
|
|commercial (free in United Kingdom)
|-
|[[CCP5 Program Library]]
|various
|program library
|free to academics
|-
|[[CHARMM]]
|
|'''C'''hemistry at '''HAR'''vard '''M'''olecular '''M'''echanics
|commercial
|-
|[[CPMD]]
|[[ab initio molecular dynamics]]
|'''C'''arr-'''P'''arrinello '''M'''olecular '''D'''ynamics
|free with [http://www.cpmd.org/cpmd_licence.html license]
|-
|[[Dalton]]
|
|Computational chemistry
|free with [http://www.theochem.kth.se/dalton/ license]
|-
|[[DiMol2D]]
|[[molecular dynamics]]
|Molecular dynamics visualization
|free executable
|-
|[[DL_MESO]]
|[[dissipative particle dynamics]]
|Mesoscale simulation package
|free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_MESO/Registration.shtml academic license]
|-
|[[DL_POLY]]
|[[molecular dynamics]]
|Molecular simulation package
|free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/Registration.shtml academic license]
|-
|[[DYNAMO]]
|[[molecular dynamics]]
|[[Event-driven molecular dynamics]]
|free source
|-
|[[EGO VIII]]
|[[molecular dynamics]]
|
|free
|-
|[[ENCAD]]
|[[molecular dynamics]]
|'''En'''ergy '''Ca'''lculation and '''D'''ynamics
|
|-
|[[ESPResSo]]
|[[molecular dynamics]]
|'''E'''xtensible '''S'''imulation '''P'''ackage for '''Res'''earch on '''So'''ft matter
|free
|-
|[[Etomica]]
|
|development environment
|free
|-
|[[FOCUS]]
|molecular dynamics analysis
|
|
|-
|[[Gaussian]]
|electronic structure
|Computational chemistry
|commercial
|-
|[[gdpc]]
|visualisation
|molecular dynamics visualisation
|free (GNU license)
|-
|[[GROMACS]]
|[[molecular dynamics]]
|
|free source
|-
|[[GROMOS]]
|[[molecular dynamics]]
|biomolecular systems
|free for academics, fee otherwise
|-
|[[GULP]]
|[[lattice dynamics]]
|'''G'''eneral '''U'''tility '''L'''attice '''P'''rogram
|free for academics, fee otherwise
|-
|[[HOOMD]]
|[[molecular dynamics]]
|'''H'''ighly '''O'''ptimized '''O'''bject Oriented '''M'''olecular '''D'''ynamics.
|free, Open Source
|-
|[[IMD]]
|[[molecular dynamics]]
|
|
|-
|[[Jmol]]
|visualisation
|
|free
|-
|[[LAMMPS]]
|[[molecular dynamics]]
|
|free source (GNU license)
|-
|[[MACSIMUS]]
|[[molecular dynamics]]
|'''MAC'''romolecule '''SIMU'''lation '''S'''oftware
|free
|-
|[[Materials Studio]]
|various
|
|commercial
|-
|[[MCCCS Towhee]]
|[[Monte Carlo]]
|
|free source
|-
|[[MCPRO]]
|[[Monte Carlo]]
|peptides, proteins, and nucleic acids in solution
|commercial
|-
|[[MDynaMix]]
|[[molecular dynamics]]
|molecular dynamics of mixtures
|free (GNU license)
|-
|[[MOIL]]
|[[molecular dynamics]]
|
|Open Source
|-
|[[Moldy]]
|[[molecular dynamics]]
|
|free
|-
|[[Molecular Workbench]]
|
|Interactive simulations
|free, Open Source
|-
|[[Moscito]]
|[[molecular dynamics]]
|
|free (General Public License)
|-
|[[Music]]
|
|'''Mu'''ltipurpose '''Si'''mulation '''C'''ode
|free (General Public License)
|-
|[[NAMD]]
|[[molecular dynamics]]
|
|free
|-
|[[NWChem]]
|
|Computational chemistry
|free
|-
|[[OpenMD]]
|[[molecular dynamics]]
|
|free - Open Source
|-
|[[ORAC]]
|[[molecular dynamics]]
|
|free
|-
|[[Packmol]]
|[[molecular dynamics]]
|creates an initial configuration for use in simulations
|free (GNU license)
|-
|[[Peacemaker]]
|statistical thermodynamics
|Quantum cluster equilibrium calculations.
|free (GNU GPL v3)
|-
|[[PINY_MD]]
|[[molecular dynamics]]
|
|free
|-
|[[Protein Explorer]]
|visualisation
|molecular graphics
|free
|-
|[http://www.pymol.org/ PyMol]
|visualisation
|molecular graphics
|commercial (academic: free)
|-
|[[Q molecular dynamics program | Q]] ([http://xray.bmc.uu.se/~aqwww/q/ link])
|[[molecular dynamics]]
|[[Helmholtz energy function |free energy]] calculations in [[Biological systems | biomolecular systems]]
|free with [http://xray.bmc.uu.se/~aqwww/q/q_license.pdf licence]
|-
|[[QMGA]]
|visualisation
|molecular graphics
|free source
|-
|[[RasMol]]
|visualisation
|molecular graphics
|free source
|-
|[[RedMD]]
|[[molecular dynamics]]
|'''Red'''uced '''M'''olecular '''D'''ynamics
|free, Open source
|-
|[[SageMD]]
|simulation front and back end
|
|
|-
|[[SIESTA]]
|[[ab initio molecular dynamics]]
|'''S'''panish '''I'''nitiative for '''E'''lectronic '''S'''imulations with '''T'''housands of '''A'''toms
|free for academics, fee otherwise
|-
|[[SMMP]]
|[[Monte Carlo]]
|'''S'''imple '''M'''olecular '''M'''echanics for '''P'''roteins
|free (General Public License) with restrictions
|-
|[[SYBYL]]
|various
|
|commercial
|-
|[[Tesla Bio Workbench]]
|
|GPU computing
|
|-
|[[TINKER]]
|
|Software tools for molecular design
|free source
|-
|[[UHBD]]
|[[brownian dynamics]]
|'''U'''niversity of '''H'''ouston '''B'''rownian '''D'''ynamics
|license required
|-
|[[VASP]]
|[[ab initio molecular dynamics]]
|
|
|-
|[[VMD]]
|visualisation
|Molecular dynamics visualisation in 3-dimensions
|free
|-
|[[WIEN2K]]
|
|Electronic structure calculation in solids
|commercial
|-
|[[XCrysDen]]
|visualisation
|Crystalline and molecular structure visualisation
|free (General Public License)
|-
|[http://www.nongnu.org/xmakemol/ XMakemol]
|visualisation
|
|free
|-
|[[X-PLOR]]
|
|Computational structural biology
|
|-
|[[YASARA]]
|
|
|free & commercial
|-
|[http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html YASP]
|[[molecular dynamics]]
|
|
|}

<references/>
[[category: Materials modelling and computer simulation codes]]

Materials modelling and computer simulation codes

2011-10-19T15:51:15Z

Mdlugosz:

The following is a sortable list (to change sort criteria click on the square icon next to the column title) of software for use in materials modelling and computer simulation. The use of simulation software whose source code you have access to (for example, Open Source, or GNU General Public License) is a fundamental tenet of good practice, and is highly recommended <ref>[http://dx.doi.org/10.1063/1.476021 Wilfred F. van Gunsteren, and Alan E. Mark "Validation of molecular dynamics simulation", Journal of Chemical Physics '''108''' pp. 6109-6116 (1998)]</ref>.
{| class="wikitable sortable" border="1" cellpadding="5" cellspacing="0"
|-
! Computer program !! Focus !! class="unsortable" | Notes !! License
|-
|[[Abalone]]
|[[molecular dynamics]], visualisation
|biopolimers
|Free
|-
|[[ACEMD]]
|[[molecular dynamics]]
|biopolimers
|free/commercial
|-
|[[AMBER -- Assisted Model Building with Energy Refinement | AMBER]]
|[[molecular dynamics]]
|Assisted Model Building with Energy Refinement
|commercial
|-
|[[BD_BOX]]
|
|an open source, scalable Brownian dynamics package for UNIX/LINUX platforms
|GNU Public License
|-
|[[BOSS]]
|
| '''B'''iochemical and '''O'''rganic '''S'''imulation '''S'''ystem
|commercial
|-
|[[BRAHMS]]
|[[molecular dynamics]]
|'''B'''iomembrane '''R'''educed-'''A'''pproac'''H''' '''M'''olecular '''S'''imulator
|in development
|-
|[[CASTEP]]
|[[density-functional theory]]
|
|commercial (free in United Kingdom)
|-
|[[CCP5 Program Library]]
|various
|program library
|free to academics
|-
|[[CHARMM]]
|
|'''C'''hemistry at '''HAR'''vard '''M'''olecular '''M'''echanics
|commercial
|-
|[[CPMD]]
|[[ab initio molecular dynamics]]
|'''C'''arr-'''P'''arrinello '''M'''olecular '''D'''ynamics
|free with [http://www.cpmd.org/cpmd_licence.html license]
|-
|[[Dalton]]
|
|Computational chemistry
|free with [http://www.theochem.kth.se/dalton/ license]
|-
|[[DiMol2D]]
|[[molecular dynamics]]
|Molecular dynamics visualization
|free executable
|-
|[[DL_MESO]]
|[[dissipative particle dynamics]]
|Mesoscale simulation package
|free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_MESO/Registration.shtml academic license]
|-
|[[DL_POLY]]
|[[molecular dynamics]]
|Molecular simulation package
|free source with [http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/Registration.shtml academic license]
|-
|[[DYNAMO]]
|[[molecular dynamics]]
|[[Event-driven molecular dynamics]]
|free source
|-
|[[EGO VIII]]
|[[molecular dynamics]]
|
|free
|-
|[[ENCAD]]
|[[molecular dynamics]]
|'''En'''ergy '''Ca'''lculation and '''D'''ynamics
|
|-
|[[ESPResSo]]
|[[molecular dynamics]]
|'''E'''xtensible '''S'''imulation '''P'''ackage for '''Res'''earch on '''So'''ft matter
|free
|-
|[[Etomica]]
|
|development environment
|free
|-
|[[FOCUS]]
|molecular dynamics analysis
|
|
|-
|[[Gaussian]]
|electronic structure
|Computational chemistry
|commercial
|-
|[[gdpc]]
|visualisation
|molecular dynamics visualisation
|free (GNU license)
|-
|[[GROMACS]]
|[[molecular dynamics]]
|
|free source
|-
|[[GROMOS]]
|[[molecular dynamics]]
|biomolecular systems
|free for academics, fee otherwise
|-
|[[GULP]]
|[[lattice dynamics]]
|'''G'''eneral '''U'''tility '''L'''attice '''P'''rogram
|free for academics, fee otherwise
|-
|[[HOOMD]]
|[[molecular dynamics]]
|'''H'''ighly '''O'''ptimized '''O'''bject Oriented '''M'''olecular '''D'''ynamics.
|free, Open Source
|-
|[[IMD]]
|[[molecular dynamics]]
|
|
|-
|[[Jmol]]
|visualisation
|
|free
|-
|[[LAMMPS]]
|[[molecular dynamics]]
|
|free source (GNU license)
|-
|[[MACSIMUS]]
|[[molecular dynamics]]
|'''MAC'''romolecule '''SIMU'''lation '''S'''oftware
|free
|-
|[[Materials Studio]]
|various
|
|commercial
|-
|[[MCCCS Towhee]]
|[[Monte Carlo]]
|
|free source
|-
|[[MCPRO]]
|[[Monte Carlo]]
|peptides, proteins, and nucleic acids in solution
|commercial
|-
|[[MDynaMix]]
|[[molecular dynamics]]
|molecular dynamics of mixtures
|free (GNU license)
|-
|[[MOIL]]
|[[molecular dynamics]]
|
|Open Source
|-
|[[Moldy]]
|[[molecular dynamics]]
|
|free
|-
|[[Molecular Workbench]]
|
|Interactive simulations
|free, Open Source
|-
|[[Moscito]]
|[[molecular dynamics]]
|
|free (General Public License)
|-
|[[Music]]
|
|'''Mu'''ltipurpose '''Si'''mulation '''C'''ode
|free (General Public License)
|-
|[[NAMD]]
|[[molecular dynamics]]
|
|free
|-
|[[NWChem]]
|
|Computational chemistry
|free
|-
|[[OpenMD]]
|[[molecular dynamics]]
|
|free - Open Source
|-
|[[ORAC]]
|[[molecular dynamics]]
|
|free
|-
|[[Packmol]]
|[[molecular dynamics]]
|creates an initial configuration for use in simulations
|free (GNU license)
|-
|[[Peacemaker]]
|statistical thermodynamics
|Quantum cluster equilibrium calculations.
|free (GNU GPL v3)
|-
|[[PINY_MD]]
|[[molecular dynamics]]
|
|free
|-
|[[Protein Explorer]]
|visualisation
|molecular graphics
|free
|-
|[http://www.pymol.org/ PyMol]
|visualisation
|molecular graphics
|commercial (academic: free)
|-
|[[Q molecular dynamics program | Q]] ([http://xray.bmc.uu.se/~aqwww/q/ link])
|[[molecular dynamics]]
|[[Helmholtz energy function |free energy]] calculations in [[Biological systems | biomolecular systems]]
|free with [http://xray.bmc.uu.se/~aqwww/q/q_license.pdf licence]
|-
|[[QMGA]]
|visualisation
|molecular graphics
|free source
|-
|[[RasMol]]
|visualisation
|molecular graphics
|free source
|-
|[[RedMD]]
|[[molecular dynamics]]
|'''Red'''uced '''M'''olecular '''D'''ynamics
|free, Open source
|-
|[[SageMD]]
|simulation front and back end
|
|
|-
|[[SIESTA]]
|[[ab initio molecular dynamics]]
|'''S'''panish '''I'''nitiative for '''E'''lectronic '''S'''imulations with '''T'''housands of '''A'''toms
|free for academics, fee otherwise
|-
|[[SMMP]]
|[[Monte Carlo]]
|'''S'''imple '''M'''olecular '''M'''echanics for '''P'''roteins
|free (General Public License) with restrictions
|-
|[[SYBYL]]
|various
|
|commercial
|-
|[[Tesla Bio Workbench]]
|
|GPU computing
|
|-
|[[TINKER]]
|
|Software tools for molecular design
|free source
|-
|[[UHBD]]
|[[brownian dynamics]]
|'''U'''niversity of '''H'''ouston '''B'''rownian '''D'''ynamics
|license required
|-
|[[VASP]]
|[[ab initio molecular dynamics]]
|
|
|-
|[[VMD]]
|visualisation
|Molecular dynamics visualisation in 3-dimensions
|free
|-
|[[WIEN2K]]
|
|Electronic structure calculation in solids
|commercial
|-
|[[XCrysDen]]
|visualisation
|Crystalline and molecular structure visualisation
|free (General Public License)
|-
|[http://www.nongnu.org/xmakemol/ XMakemol]
|visualisation
|
|free
|-
|[[X-PLOR]]
|
|Computational structural biology
|
|-
|[[YASARA]]
|
|
|free & commercial
|-
|[http://www.theo.chemie.tu-darmstadt.de/group/services/yaspdoc/yaspdoc.html YASP]
|[[molecular dynamics]]
|
|
|}

<references/>
[[category: Materials modelling and computer simulation codes]]