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List of software for Monte Carlo molecular modeling

From Wikipedia, the free encyclopedia

This is a list of computer programs that useMonte Carlo methods formolecular modeling.

See also

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References

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  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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