List of software for Monte Carlo molecular modeling

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

  • Cassandra classical[2]
  • FEASST classical[3]
  • GOMC classical[4]
  • TransRot classical[18]
  • Towhee classical[19]
  • TurboRVB quantum[20]

See also

[edit]

References

[edit]
  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. PMID 21386247.
  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. Bibcode:2017JCoCh..38.1727S. 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 123004: 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. PMID 8289329.
  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. ^ Wheeler, William A.; Pathak, Shivesh; Kleiner, Kevin G.; Yuan, Shunyue; Rodrigues, João N. B.; Lorsung, Cooper; Krongchon, Kittithat; Chang, Yueqing; Zhou, Yiqing; Busemeyer, Brian; Williams, Kiel T.; Muñoz, Alexander; Chow, Chun Yu; Wagner, Lucas K. (21 March 2023). "PyQMC : An all-Python real-space quantum Monte Carlo module in PySCF". The Journal of Chemical Physics. 158 (11) 114801. arXiv:2212.01482. Bibcode:2023JChPh.158k4801W. doi:10.1063/5.0139024. PMID 36948839.
  11. ^ 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.
  12. ^ Scemama, Anthony; Caffarel, Michel; Oseret, Emmanuel; Jalby, William (2013). "QMC=Chem: A Quantum Monte Carlo Program for Large-Scale Simulations in Chemistry at the Petascale Level and beyond". High Performance Computing for Computational Science - VECPAR 2012. Lecture Notes in Computer Science. Vol. 7851. pp. 118–127. doi:10.1007/978-3-642-38718-0_14. ISBN 978-3-642-38717-3.
  13. ^ Scemama, Anthony; Caffarel, Michel; Oseret, Emmanuel; Jalby, William (30 April 2013). "Quantum Monte Carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond". Journal of Computational Chemistry. 34 (11): 938–951. arXiv:1209.6630. Bibcode:2013JCoCh..34..938S. doi:10.1002/jcc.23216. PMID 23288704.
  14. ^ 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.
  15. ^ Kent, P. R. C.; Annaberdiyev, Abdulgani; Benali, Anouar; Bennett, M. Chandler; Landinez Borda, Edgar Josué; Doak, Peter; Hao, Hongxia; Jordan, Kenneth D.; Krogel, Jaron T.; Kylänpää, Ilkka; Lee, Joonho; Luo, Ye; Malone, Fionn D.; Melton, Cody A.; Mitas, Lubos; Morales, Miguel A.; Neuscamman, Eric; Reboredo, Fernando A.; Rubenstein, Brenda; Saritas, Kayahan; Upadhyay, Shiv; Wang, Guangming; Zhang, Shuai; Zhao, Luning (7 May 2020). "QMCPACK: Advances in the development, efficiency, and application of auxiliary field and real-space variational and diffusion quantum Monte Carlo". The Journal of Chemical Physics. 152 (17) 174105. arXiv:2003.01831. Bibcode:2020JChPh.152q4105K. doi:10.1063/5.0004860. PMID 32384844.
  16. ^ Barborini, Matteo; Charry, Jorge; Ditte, Matej; Leventis, Andronikos; Kafanas, Georgios; Tkatchenko, Alexandre (30 Jan 2026). "QMeCha: quantum Monte Carlo package for fermions in embedding environments". The Journal of Chemical Physics. 164 (6) 062501. arXiv:2511.03439. doi:10.1063/5.0311994. PMID 41677286.
  17. ^ Wagner, Lucas K.; Bajdich, Michal; Mitas, Lubos (May 2009). "QWalk: A quantum Monte Carlo program for electronic structure". Journal of Computational Physics. 228 (9): 3390–3404. Bibcode:2009JCoPh.228.3390W. doi:10.1016/j.jcp.2009.01.017.
  18. ^ 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}: CS1 maint: work parameter with ISBN (link)
  19. ^ 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. Bibcode:2013MoSim..39.1212M. doi:10.1080/08927022.2013.828208. S2CID 97160184.
  20. ^ Nakano, Kousuke; Attaccalite, Claudio; Barborini, Matteo; Capriotti, Luca; Casula, Michele; Coccia, Emanuele; Dagrada, Mario; Genovese, Claudio; Luo, Ye; Mazzola, Guglielmo; Zen, Andrea; Sorella, Sandro (29 May 2020). "TurboRVB : A many-body toolkit for ab initio electronic simulations by quantum Monte Carlo". The Journal of Chemical Physics. 152 (20) 204121. arXiv:2002.07401. Bibcode:2020JChPh.152t4121N. doi:10.1063/5.0005037. PMID 32486669.

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