MDynaMix
DNA simulation on MDynaMix
MDynaMix [1] [2] (an acronym for Molecular Dynamics of Mixtures) is a general purpose molecular dynamics software package for simulations mixtures of molecules, interacting by AMBER/CHARMM like force fields in a periodic boundary conditions. MDynaMix is developed at the Stockholm University, Sweden. Algorithms for NVE, NVT, NPT and anisotropic NPT ensembles are employed, as well as Ewald summation for treatment of the electrostatic interactions. The code was written in Fortran 77 (with MPI for parallel execution) and C++ and released under the GNU GPL. The package works on Unix/Linux workstations and clusters of workstations as well as on Windows in sequential mode.
Programs
- md - the main MDynaMix block
- makemol is a utility which provides help in creation of files describing molecular structure and the force field
- tranal is a suite of utilities for analyzing trajectories
- mdee is a version of the program which implement expanded ensemble method for computation of free energy/ chemical potential (is not parallelized)
- mge provides graphical interface for molecular models construction and monitoring of dynamics process
Field of application
- Thermodynamic properties of liquids [3]
- Nucleic acid - ions interaction [4]
- Modeling of lipid bilayers[5]
- Polyelectrolytes[6]
- Ionic liquids[7][8]
- X-ray spectra of liquid water[9]
- Force Field development[10][11]
See also
References
- ↑ 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. 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 1541. Heidelberg: Springer Berlin. pp. 296–303. doi:10.1007/BFb0095310. ISBN 978-3-540-65414-8.
- ↑ T. Kuznetsova and B. Kvamme (2002). "Thermodynamic properties and interfacial tension of a model water–carbon dioxide system". Phys. Chem. Chem. Phys. 4 (6): 937–941. doi:10.1039/b108726f.
- ↑ Y. Cheng, N. Korolev and 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 and 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.
- ↑ A. Vishnyakov and 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. doi:10.1063/1.2899327. PMID 18447495.
- ↑ G. Raabe and J. Köhler (2008). "Thermodynamical and structural properties of imidazolium based ionic liquids from molecular simulation". J. Chem. Phys. 128 (15): 154509. doi:10.1063/1.2907332. PMID 18433237.
- ↑ X. Wu, Z. Liu, S. Huang and 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. doi:10.1039/b504681p. PMID 16189592.
- ↑ R.L.C. Wang, H.J. Kreuzer and M. Grunze (2006). "Theoretical modeling and interpretation of X-ray absorption spectra of liquid water". Phys. Chem. Chem. Phys. 8 (41): 4744–4751. doi:10.1039/b607093k. PMID 17043717.
- ↑ A.M. Nikitin and A.P. Lyubartsev (2007). "A new six-site acetonitrile model for simulations of liquid acetonitril and its aqueous mixture". J. Comp. Chem. 28 (12): 2020–2026. doi:10.1002/jcc.20721. PMID 17450554.
- ↑ 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: 101–113. doi:10.1016/j.chemphys.2007.12.006.