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MDynaMix
Software for modelling molecules
Software for modelling molecules
| Field | Value |
|---|---|
| name | Molecular Dynamics of Mixtures |
| logo | |
| screenshot | Image:MDynaMix-MGE.png |
| screenshot alt | Computer display showing temperature function on left, DNA molecule in center, and various menu items to right and below. |
| caption | DNA simulation on MDynaMix |
| author | Aatto Laaksonen, Alexander Lyubartsev |
| developer | Stockholm University, Department of Materials and Environmental Chemistry, Division of Physical Chemistry |
| released | |
| latest release version | 5.3.0 |
| latest release date | {{cite web |
| url | http://www.fos.su.se/~sasha/mdynamix/ |
| title | MDynaMix Homepage |
| website | fos.su.se |
| access-date | 2021-04-15 |
| latest preview date | |
| programming language | Fortran 77-90 |
| operating system | Unix, Unix-like, Linux, Windows |
| platform | x86, x86-64, Cray |
| language | English |
| genre | Molecular dynamics |
| license | GPL |
| website | |
| repo |
| access-date = 2021-04-15 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.{{cite book |title= Applied Parallel Computing Large Scale Scientific and Industrial Problems 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.
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
- 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
- Thermodynamic properties of liquids{{cite journal
- Nucleic acid - ions interaction{{cite journal
- Modeling of lipid bilayers{{cite journal
- Polyelectrolytes{{cite journal
- Ionic liquids{{cite journal
- X-ray spectra of liquid water{{cite journal
- Force Field development{{cite journal
References
References
- A.P.Lyubartsev, A.Laaksonen. (2000). "MDynaMix - A scalable portable parallel MD simulation package for arbitrary molecular mixtures". Computer Physics Communications.
This article was imported from Wikipedia and is available under the Creative Commons Attribution-ShareAlike 4.0 License. Content has been adapted to SurfDoc format. Original contributors can be found on the article history page.
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