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MDynaMix

From Wikipedia, the free encyclopedia
Software for modelling molecules
Molecular Dynamics of Mixtures
Computer display showing temperature function on left, DNA molecule in center, and various menu items to right and below.
DNA simulation on MDynaMix
Original authorsAatto Laaksonen, Alexander Lyubartsev
DevelopersStockholm University, Department of Materials and Environmental Chemistry, Division of Physical Chemistry
Initial release1993; 33 years ago (1993)
Stable release
5.3.0 / 15 January 2019; 7 years ago (2019-01-15)[1]
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

Molecular Dynamics of Mixtures (MDynaMix) is a computersoftware package for general purposemolecular dynamics to simulate mixtures of molecules, interacting byAMBER- andCHARMM-likeforce fields inperiodic boundary conditions.[2][3]Algorithms are included for NVE, NVT, NPT, anisotropic NPT ensembles, andEwald summation to treat electrostatic interactions.The code was written in a mix ofFortran 77 and 90 (withMessage Passing Interface (MPI) for parallel execution). The package runs onUnix andUnix-like (Linux) workstations, clusters of workstations, and onWindows in sequential mode.

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

Programs

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Field of application

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See also

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References

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  1. ^"MDynaMix Homepage".fos.su.se. Retrieved2021-04-15.
  2. ^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.
  3. ^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. Vol. 1541. Heidelberg: Springer Berlin. pp. 296–303.doi:10.1007/BFb0095310.ISBN 978-3-540-65414-8.S2CID 26892490.
  4. ^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.
  5. ^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.
  6. ^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.S2CID 8599984.
  7. ^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.S2CID 948639.
  8. ^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.
  9. ^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.
  10. ^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.
  11. ^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.S2CID 5333395.
  12. ^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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