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.[2][3] 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.
 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 release | 1993 |
| Stable release | 5.3.0
/ 15 January 2019[1] |
| Written in | Fortran 77-90 |
| Operating system | Unix, Unix-like, Linux, Windows |
| Platform | x86, x86-64, Cray |
| Available in | English |
| Type | Molecular dynamics |
| License | GPL |
| Website | www |
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
edit- md is the main MDynaMix block
- makemol is a utility which provides help to create files describing molecular structure and the force field
- tranal is a suite of utilities to analyze trajectories
- mdee is a version of the program which implements expanded ensemble method to compute free energy and chemical potential (is not parallelized)
- mge provides a graphical user interface to construct molecular models and monitor dynamics process
Field of application
edit- Thermodynamic properties of liquids[4]
- Nucleic acid - ions interaction[5]
- Modeling of lipid bilayers[6]
- Polyelectrolytes[7]
- Ionic liquids[8][9]
- X-ray spectra of liquid water[10]
- Force Field development[11][12]
See also
edit
References
edit- ^ "MDynaMix Homepage". fos.su.se. Retrieved 2021-04-15.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.