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.

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<span class="mw-page-title-main">PLATO (computational chemistry)</span>

PLATO is a suite of programs for electronic structure calculations. It receives its name from the choice of basis set used to expand the electronic wavefunctions.

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Auxiliary-field Monte Carlo is a method that allows the calculation, by use of Monte Carlo techniques, of averages of operators in many-body quantum mechanical or classical problems.

Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of Message Passing Interface (MPI) for parallel communication and is free and open-source software, distributed under the terms of the GNU General Public License.

Path integral Monte Carlo (PIMC) is a quantum Monte Carlo method used to solve quantum statistical mechanics problems numerically within the path integral formulation. The application of Monte Carlo methods to path integral simulations of condensed matter systems was first pursued in a key paper by John A. Barker.

FLUKA is a fully integrated Monte Carlo simulation package for the interaction and transport of particles and nuclei in matter. FLUKA has many applications in particle physics, high energy experimental physics and engineering, shielding, detector and telescope design, cosmic ray studies, dosimetry, medical physics, radiobiology. A recent line of development concerns hadron therapy.

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This is a list of computer programs that are predominantly used for molecular mechanics calculations.

<span class="mw-page-title-main">Molecular modeling on GPUs</span> Using graphics processing units for molecular simulations

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<span class="mw-page-title-main">MDynaMix</span>

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<span class="mw-page-title-main">Ascalaph Designer</span>

Ascalaph Designer is a computer program for general purpose molecular modelling for molecular design and simulations. It provides a graphical environment for the common programs of quantum and classical molecular modelling ORCA, NWChem, Firefly, CP2K and MDynaMix . The molecular mechanics calculations cover model building, energy optimizations and molecular dynamics. Firefly covers a wide range of quantum chemistry methods. Ascalaph Designer is free and open-source software, released under the GNU General Public License, version 2 (GPLv2).

Quantemol Ltd is based in University College London initiated by Professor Jonathan Tennyson FRS and Dr. Daniel Brown in 2004. The company initially developed a unique software tool, Quantemol-N, which provides full accessibility to the highly sophisticated UK molecular R-matrix codes, used to model electron polyatomic molecule interactions. Since then Quantemol has widened to further types of simulation, with plasmas and industrial plasma tools, in Quantemol-VT in 2013 and launched in 2016 a sustainable database Quantemol-DB, representing the chemical and radiative transport properties of a wide range of plasmas.

Path integral molecular dynamics (PIMD) is a method of incorporating quantum mechanics into molecular dynamics simulations using Feynman path integrals. In PIMD, one uses the Born–Oppenheimer approximation to separate the wavefunction into a nuclear part and an electronic part. The nuclei are treated quantum mechanically by mapping each quantum nucleus onto a classical system of several fictitious particles connected by springs governed by an effective Hamiltonian, which is derived from Feynman's path integral. The resulting classical system, although complex, can be solved relatively quickly. There are now a number of commonly used condensed matter computer simulation techniques that make use of the path integral formulation including Centroid Molecular Dynamics (CMD), Ring Polymer Molecular Dynamics (RPMD), and the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method. The same techniques are also used in path integral Monte Carlo (PIMC).

<span class="mw-page-title-main">James B. Anderson</span> American chemist and physicist (1935–2021)

James Bernhard Anderson was an American chemist and physicist. From 1995 to 2014 he was Evan Pugh Professor of Chemistry and Physics at the Pennsylvania State University. He specialized in Quantum Chemistry by Monte Carlo methods, molecular dynamics of reactive collisions, kinetics and mechanisms of gas phase reactions, and rare-event theory.

Massively Parallel Monte Carlo (MPMC) is a Monte Carlo method package primarily designed to simulate liquids, molecular interfaces, and functionalized nanoscale materials. It was developed originally by Jon Belof and is now maintained by a group of researchers in the Department of Chemistry and SMMARTT Materials Research Center at the University of South Florida. MPMC has been applied to the scientific research challenges of nanomaterials for clean energy, carbon sequestration, and molecular detection. Developed to run efficiently on the most powerful supercomputing platforms, MPMC can scale to extremely large numbers of CPUs or GPUs. Since 2012, MPMC has been released as an open-source software project under the GNU General Public License (GPL) version 3, and the repository is hosted on GitHub.

PLUMED is an open-source library implementing enhanced-sampling algorithms, various free-energy methods, and analysis tools for molecular dynamics simulations. It is designed to be used together with ACEMD, AMBER, DL_POLY, GROMACS, LAMMPS, NAMD, OpenMM, ABIN, CP2K, i-PI, PINY-MD, and Quantum ESPRESSO, but it can also be used together with analysis and visualization tools VMD, HTMD, and OpenPathSampling.

ms2 (software) Molecular simulation program

ms2 is a non-commercial molecular simulation program. It comprises both molecular dynamics and Monte Carlo simulation algorithms. ms2 is designed for the calculation of thermodynamic properties of fluids. A large number of thermodynamic properties can be readily computed using ms2, e.g. phase equilibrium, transport and caloric properties. ms2 is limited to homogeneous state simulations.

References

  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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