List of software for Monte Carlo molecular modeling

Last updated

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

See also

Related Research Articles

In physics, statistical mechanics is a mathematical framework that applies statistical methods and probability theory to large assemblies of microscopic entities. It does not assume or postulate any natural laws, but explains the macroscopic behavior of nature from the behavior of such ensembles.

Monte Carlo methods, or Monte Carlo experiments, are a broad class of computational algorithms that rely on repeated random sampling to obtain numerical results. The underlying concept is to use randomness to solve problems that might be deterministic in principle. The name comes from the Monte Carlo Casino in Monaco, where the primary developer of the method, physicist Stanislaw Ulam, was inspired by his uncle's gambling habits.

<span class="mw-page-title-main">Molecular dynamics</span> Computer simulations to discover and understand chemical properties

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics.

<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.

Ian Philip Grant, DPhil; FRS; CMath; FIMA, FRAS, FInstP is a British mathematical physicist. He is Emeritus Professor of Mathematical Physics at the University of Oxford and was elected a fellow of the Royal Society in 1992. He is a pioneer in the field of computational physics and is internationally recognised as the principal author of GRASP, the General Relativistic Atomic Structure Program.

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.

The Reverse Monte Carlo (RMC) modelling method is a variation of the standard Metropolis–Hastings algorithm to solve an inverse problem whereby a model is adjusted until its parameters have the greatest consistency with experimental data. Inverse problems are found in many branches of science and mathematics, but this approach is probably best known for its applications in condensed matter physics and solid state chemistry.

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.

A field-theoretic simulation is a numerical strategy to calculate structure and physical properties of a many-particle system within the framework of a statistical field theory, like e.g. a polymer field theory. A convenient possibility is to use Monte Carlo (MC) algorithms, to sample the full partition function integral expressed in field-theoretic representation. The procedure is then called the auxiliary field Monte Carlo method. However, it is well known that MC sampling in conjunction with the basic field-theoretic representation of the partition function integral, directly obtained via the Hubbard-Stratonovich transformation, is impracticable, due to the so-called numerical sign problem. The difficulty is related to the complex and oscillatory nature of the resulting distribution function, which causes a bad statistical convergence of the ensemble averages of the desired structural and thermodynamic quantities. In such cases special analytical and numerical techniques are required to accelerate the statistical convergence of the field-theoretic simulation.

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

Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.

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

Molecular Dynamics of Mixtures (MDynaMix) is a computer software package for general purpose molecular dynamics to simulate mixtures of molecules, interacting by AMBER- and CHARMM-like force fields in periodic boundary conditions. Algorithms are included for NVE, NVT, NPT, anisotropic NPT ensembles, and Ewald summation to treat electrostatic interactions. The code was written in a mix of Fortran 77 and 90. The package runs on Unix and Unix-like (Linux) workstations, clusters of workstations, and on Windows in sequential mode.

This is a list of notable computer programs that are used for nucleic acids simulations.

<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).

<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 to 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: 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. ↑ 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.
  6. ↑ 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.
  7. ↑ 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.
  8. ↑ 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.
  9. ↑ 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.
  10. ↑ 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.
  11. ↑ 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, Washington, DC: American Chemical Society, vol. 1428, pp. 19–38, doi:10.1021/bk-2022-1428.ch002, ISBN   978-0-8412-9743-2
  12. ↑ 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.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.