From Wikipedia, the free encyclopedia
This is a list of computer programs that use
Monte Carlo methods for
molecular modeling .
See also
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 .