List of software for Monte Carlo molecular modeling

This is a list of computer programs that use Monte Carlo methods for molecular modeling.

Abalone _{classical Hybrid MC}
BOSS _classical
CASINO _quantum^[1]
Cassandra _classical^[2]
CP2K
FEASST _classical^[3]
GOMC _classical^[4]

Internal_Coordinate_Mechanics ICM by MolSoft _classical^[5]

MacroModel _classical
Materials Studio _classical
ms2^[6]^[7]^[8]^[9]_classical
RASPA _classical^[10]
QMCPACK _quantum^[11]
Spartan _classical
Tinker _classical
TransRot _classical^[12]
Towhee _classical^[13]

References

^ Needs, R.J.; Towler, M.D.; Drummond, N.D.; Ríos, P. López (20 January 2010). "Continuum variational and diffusion quantum Monte Carlo calculations". J. Phys.: Condens. Matter. 22 (2): 023201. arXiv:1002.2127. doi:10.1088/0953-8984/22/2/023201.
^ Shah, Jindal K.; Marin-Rimoldi, Eliseo; Mullen, Ryan Gotchy; Keene, Brian P.; Khan, Sandip; Paluch, Andrew S.; Rai, Neeraj; Romanielo, Lucienne L.; Rosch, Thomas W.; Yoo, Brian; Maginn, Edward J. (15 July 2017). "Cassandra: An open source Monte Carlo package for molecular simulation". Journal of Computational Chemistry. 38 (19): 1727–1739. doi:10.1002/jcc.24807. PMID 28436594.
^ Hatch, Harold; Mahynski, Nathan; Shen, Vincent (1 March 2018). "FEASST: Free Energy and Advanced Sampling Simulation Toolkit". Journal of Research of the National Institute of Standards and Technology. 123: 1–3. doi:10.6028/jres.123.004. PMC 7339717. PMID 34877133.
^ Nejahi, Younes; Soroush Barhaghi, Mohammad; Mick, Jason; Jackman, Brock; Rushaidat, Kamel; Li, Yuanzhe; Schwiebert, Loren; Potoff, Jeffrey (28 November 2018). "GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids". SoftwareX. 9: 20–27. doi:10.1016/j.softx.2018.11.005.
^ Abagyan, Ruben; Totrov, Maxim (28 January 2004). "Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins". J. Mol. Biol. 21, 235(3) (3): 983–1002. doi:10.1006/jmbi.1994.1052.
^ Glass, Colin W.; Reiser, Steffen; Rutkai, Gábor; Deublein, Stephan; Köster, Andreas; Guevara-Carrion, Gabriela; Wafai, Amer; Horsch, Martin; Bernreuther, Martin; Windmann, Thorsten; Hasse, Hans (December 2014). "ms2: A molecular simulation tool for thermodynamic properties, new version release". Computer Physics Communications. 185 (12): 3302–3306. arXiv:1507.07548. Bibcode:2014CoPhC.185.3302G. doi:10.1016/j.cpc.2014.07.012. ISSN 0010-4655. S2CID 31816838.
^ Deublein, Stephan; Eckl, Bernhard; Stoll, Jürgen; Lishchuk, Sergey V.; Guevara-Carrion, Gabriela; Glass, Colin W.; Merker, Thorsten; Bernreuther, Martin; Hasse, Hans; Vrabec, Jadran (November 2011). "ms2: A molecular simulation tool for thermodynamic properties". Computer Physics Communications. 182 (11): 2350–2367. Bibcode:2011CoPhC.182.2350D. doi:10.1016/j.cpc.2011.04.026. ISSN 0010-4655.
^ Fingerhut, Robin; Guevara-Carrion, Gabriela; Nitzke, Isabel; Saric, Denis; Marx, Joshua; Langenbach, Kai; Prokopev, Sergei; Celný, David; Bernreuther, Martin; Stephan, Simon; Kohns, Maximilian (May 2021). "ms2: A molecular simulation tool for thermodynamic properties, release 4.0". Computer Physics Communications. 262: 107860. Bibcode:2021CoPhC.26207860F. doi:10.1016/j.cpc.2021.107860. ISSN 0010-4655. S2CID 232283889.
^ Rutkai, Gábor; Köster, Andreas; Guevara-Carrion, Gabriela; Janzen, Tatjana; Schappals, Michael; Glass, Colin W.; Bernreuther, Martin; Wafai, Amer; Stephan, Simon; Kohns, Maximilian; Reiser, Steffen (December 2017). "ms2: A molecular simulation tool for thermodynamic properties, release 3.0". Computer Physics Communications. 221: 343–351. Bibcode:2017CoPhC.221..343R. doi:10.1016/j.cpc.2017.07.025. ISSN 0010-4655.
^ Dubbeldam, David; Calero, Sofía; Ellis, Donald E.; Snurr, Randall Q. (26 February 2015). "RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials". Molecular Simulation. 42 (2): 81–101. doi:10.1080/08927022.2015.1010082. ISSN 0892-7022. S2CID 53077055. Wikidata Q60395799.
^ Kim, J.; et al. (QMCPACK) (27 March 2018). "QMCPACK : An open source ab initio Quantum Monte Carlo package for the electronic structure of atoms, molecules, and solids". Journal of Physics: Condensed Matter. 30 (19): 195901. arXiv:1802.06922. Bibcode:2018JPCM...30s5901K. doi:10.1088/1361-648X/aab9c3. PMID 29582782. S2CID 4913347.
^ Topper, Robert Q.; Topper, Steven L.; Lee, Sangjoon (2022-11-21), Parish, Carol A.; Hopkins, Todd A. (eds.), "TransRot: A Portable Software Package for Simulated Annealing Monte Carlo Geometry Optimization of Atomic and Molecular Clusters", ACS Symposium Series, vol. 1428, Washington, DC: American Chemical Society, pp. 19–38, doi:10.1021/bk-2022-1428.ch002, ISBN 978-0-8412-9743-2
^ Martin, Marcus G.; et al. (Towhee) (16 September 2013). "MCCCS Towhee: a tool for Monte Carlo molecular simulation". Molecular Simulation. 39 (14–15): 1212–1222. doi:10.1080/08927022.2013.828208. S2CID 97160184.

[1] Needs, R.J.; Towler, M.D.; Drummond, N.D.; Ríos, P. López (20 January 2010). "Continuum variational and diffusion quantum Monte Carlo calculations". J. Phys.: Condens. Matter. 22 (2): 023201. arXiv:1002.2127. doi:10.1088/0953-8984/22/2/023201.

[2] Shah, Jindal K.; Marin-Rimoldi, Eliseo; Mullen, Ryan Gotchy; Keene, Brian P.; Khan, Sandip; Paluch, Andrew S.; Rai, Neeraj; Romanielo, Lucienne L.; Rosch, Thomas W.; Yoo, Brian; Maginn, Edward J. (15 July 2017). "Cassandra: An open source Monte Carlo package for molecular simulation". Journal of Computational Chemistry. 38 (19): 1727–1739. doi:10.1002/jcc.24807. PMID 28436594.

[3] Hatch, Harold; Mahynski, Nathan; Shen, Vincent (1 March 2018). "FEASST: Free Energy and Advanced Sampling Simulation Toolkit". Journal of Research of the National Institute of Standards and Technology. 123: 1–3. doi:10.6028/jres.123.004. PMC 7339717. PMID 34877133.

[4] Nejahi, Younes; Soroush Barhaghi, Mohammad; Mick, Jason; Jackman, Brock; Rushaidat, Kamel; Li, Yuanzhe; Schwiebert, Loren; Potoff, Jeffrey (28 November 2018). "GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids". SoftwareX. 9: 20–27. doi:10.1016/j.softx.2018.11.005.

[5] Abagyan, Ruben; Totrov, Maxim (28 January 2004). "Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins". J. Mol. Biol. 21, 235(3) (3): 983–1002. doi:10.1006/jmbi.1994.1052.

[6] Glass, Colin W.; Reiser, Steffen; Rutkai, Gábor; Deublein, Stephan; Köster, Andreas; Guevara-Carrion, Gabriela; Wafai, Amer; Horsch, Martin; Bernreuther, Martin; Windmann, Thorsten; Hasse, Hans (December 2014). "ms2: A molecular simulation tool for thermodynamic properties, new version release". Computer Physics Communications. 185 (12): 3302–3306. arXiv:1507.07548. Bibcode:2014CoPhC.185.3302G. doi:10.1016/j.cpc.2014.07.012. ISSN 0010-4655. S2CID 31816838.

[7] Deublein, Stephan; Eckl, Bernhard; Stoll, Jürgen; Lishchuk, Sergey V.; Guevara-Carrion, Gabriela; Glass, Colin W.; Merker, Thorsten; Bernreuther, Martin; Hasse, Hans; Vrabec, Jadran (November 2011). "ms2: A molecular simulation tool for thermodynamic properties". Computer Physics Communications. 182 (11): 2350–2367. Bibcode:2011CoPhC.182.2350D. doi:10.1016/j.cpc.2011.04.026. ISSN 0010-4655.

[8] Fingerhut, Robin; Guevara-Carrion, Gabriela; Nitzke, Isabel; Saric, Denis; Marx, Joshua; Langenbach, Kai; Prokopev, Sergei; Celný, David; Bernreuther, Martin; Stephan, Simon; Kohns, Maximilian (May 2021). "ms2: A molecular simulation tool for thermodynamic properties, release 4.0". Computer Physics Communications. 262: 107860. Bibcode:2021CoPhC.26207860F. doi:10.1016/j.cpc.2021.107860. ISSN 0010-4655. S2CID 232283889.

[9] Rutkai, Gábor; Köster, Andreas; Guevara-Carrion, Gabriela; Janzen, Tatjana; Schappals, Michael; Glass, Colin W.; Bernreuther, Martin; Wafai, Amer; Stephan, Simon; Kohns, Maximilian; Reiser, Steffen (December 2017). "ms2: A molecular simulation tool for thermodynamic properties, release 3.0". Computer Physics Communications. 221: 343–351. Bibcode:2017CoPhC.221..343R. doi:10.1016/j.cpc.2017.07.025. ISSN 0010-4655.

[10] Dubbeldam, David; Calero, Sofía; Ellis, Donald E.; Snurr, Randall Q. (26 February 2015). "RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials". Molecular Simulation. 42 (2): 81–101. doi:10.1080/08927022.2015.1010082. ISSN 0892-7022. S2CID 53077055. Wikidata Q60395799.

[11] Kim, J.; et al. (QMCPACK) (27 March 2018). "QMCPACK : An open source ab initio Quantum Monte Carlo package for the electronic structure of atoms, molecules, and solids". Journal of Physics: Condensed Matter. 30 (19): 195901. arXiv:1802.06922. Bibcode:2018JPCM...30s5901K. doi:10.1088/1361-648X/aab9c3. PMID 29582782. S2CID 4913347.

[12] Topper, Robert Q.; Topper, Steven L.; Lee, Sangjoon (2022-11-21), Parish, Carol A.; Hopkins, Todd A. (eds.), "TransRot: A Portable Software Package for Simulated Annealing Monte Carlo Geometry Optimization of Atomic and Molecular Clusters", ACS Symposium Series, vol. 1428, Washington, DC: American Chemical Society, pp. 19–38, doi:10.1021/bk-2022-1428.ch002, ISBN 978-0-8412-9743-2

[13] Martin, Marcus G.; et al. (Towhee) (16 September 2013). "MCCCS Towhee: a tool for Monte Carlo molecular simulation". Molecular Simulation. 39 (14–15): 1212–1222. doi:10.1080/08927022.2013.828208. S2CID 97160184.

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v t e Computer simulation software
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List of software for Monte Carlo molecular modeling

See also

References