MDynaMix

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.[1][2] 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 (with Message Passing Interface (MPI) for parallel execution). The package runs on Unix and Unix-like (Linux) workstations, clusters of workstations, and on Windows in sequential mode.

Molecular Dynamics of Mixtures
DNA simulation on MDynaMix
Original author(s)Aatto Laaksonen, Alexander Lyubartsev
Developer(s)Stockholm University, Department of Materials and Environmental Chemistry, Division of Physical Chemistry
Initial release1993 (1993)
Stable release
5.2.7 / 31 January 2015 (2015-01-31)
Written inFortran 77-90
Operating systemUnix, Unix-like, Linux, Windows
Platformx86, x86-64, Cray
Available inEnglish
TypeMolecular dynamics
LicenseGPL
Websitewww.fos.su.se/~sasha/mdynamix

MDynaMix is developed at the Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, Sweden. It is released as open-source software under a GNU General Public License (GPL).

Programs

Field of application
gollark: "Simple" does not imply "fast to write" (look at Go, although it's more surface-level simple).
gollark: Æ.
gollark: Some of the time it's just stupid, like in `let`s.
gollark: Well, yes, via macros probably.
gollark: You basically directly write the ASTs. This requires many brackets.

See also

References
  1. A.P.Lyubartsev, A.Laaksonen (2000). "MDynaMix - A scalable portable parallel MD simulation package for arbitrary molecular mixtures". Computer Physics Communications. 128 (3): 565–589. Bibcode:2000CoPhC.128..565L. doi:10.1016/S0010-4655(99)00529-9.
  2. A.P.Lyubartsev, A.Laaksonen (1998). "Parallel molecular dynamics simulations of biomolecular systems". Applied Parallel Computing Large Scale Scientific and Industrial Problems. Lecture Notes in Computer Science. 1541. Heidelberg: Springer Berlin. pp. 296–303. doi:10.1007/BFb0095310. ISBN 978-3-540-65414-8.
  3. T. Kuznetsova & B. Kvamme (2002). "Thermodynamic properties and interfacial tension of a model water–carbon dioxide system". Phys. Chem. Chem. Phys. 4 (6): 937–941. Bibcode:2002PCCP....4..937K. doi:10.1039/b108726f.
  4. Y. Cheng, N. Korolev & L. Nordenskiöld (2006). "Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study". Nucleic Acids Research. 34 (2): 686–696. doi:10.1093/nar/gkj434. PMC 1356527. PMID 16449204.
  5. C.-J. Högberg; A.M.Nikitin & A.P. Lyubartsev (2008). "Modification of the CHARMM force field for DMPC lipid bilayer". Journal of Computational Chemistry. 29 (14): 2359–2369. doi:10.1002/jcc.20974. PMID 18512235.
  6. A. Vishnyakov & A.V. Neimark (2008). "Specifics of solvation of sulfonated polyelectrolytes in water, dimethylmethylphosphonate, and their mixture: A molecular simulation study". J. Chem. Phys. 128 (16): 164902. Bibcode:2008JChPh.128p4902V. doi:10.1063/1.2899327. PMID 18447495.
  7. G. Raabe & J. Köhler (2008). "Thermodynamical and structural properties of imidazolium based ionic liquids from molecular simulation". J. Chem. Phys. 128 (15): 154509. Bibcode:2008JChPh.128o4509R. doi:10.1063/1.2907332. PMID 18433237.
  8. X. Wu; Z. Liu; S. Huang; W. Wang (2005). "Molecular dynamics simulation of room-temperature ionic liquid mixture of [bmim][BF4] and acetonitrile by a refined force field". Phys. Chem. Chem. Phys. 7 (14): 2771–2779. Bibcode:2005PCCP....7.2771W. doi:10.1039/b504681p. PMID 16189592.
  9. R.L.C. Wang, H.J. Kreuzer & M. Grunze (2006). "Theoretical modeling and interpretation of X-ray absorption spectra of liquid water". Phys. Chem. Chem. Phys. 8 (41): 4744–4751. Bibcode:2006PCCP....8.4744W. doi:10.1039/b607093k. PMID 17043717.
  10. A.M. Nikitin & A.P. Lyubartsev (2007). "A new six-site acetonitrile model for simulations of liquid acetonitril and its aqueous mixture". J. Comput. Chem. 28 (12): 2020–2026. doi:10.1002/jcc.20721. PMID 17450554.
  11. E.S. Böesa; E. Bernardia; H. Stassena; P.F.B. Gonçalves (2008). "Solvation of monovalent anions in formamide and methanol: Parameterization of the IEF-PCM model". Chemical Physics. 344 (1–2): 101–113. Bibcode:2008CP....344..101B. doi:10.1016/j.chemphys.2007.12.006.
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