Molecular Dynamics of Mixtures (MDynaMix) is a computer
software
Software is a set of computer programs and associated documentation and data. This is in contrast to hardware, from which the system is built and which actually performs the work.
At the lowest programming level, executable code consists o ...
package for general purpose
molecular dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the s ...
to simulate mixtures of molecules, interacting by
AMBER
Amber is fossilized tree resin that has been appreciated for its color and natural beauty since Neolithic times. Much valued from antiquity to the present as a gemstone, amber is made into a variety of decorative objects."Amber" (2004). In Ma ...
- and
CHARMM
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHA ...
-like
force fields in
periodic boundary conditions
Periodic boundary conditions (PBCs) are a set of boundary conditions which are often chosen for approximating a large (infinite) system by using a small part called a ''unit cell''. PBCs are often used in computer simulations and mathematical mode ...
.
Algorithms are included for NVE, NVT, NPT, anisotropic NPT ensembles, and
Ewald summation Ewald summation, named after Paul Peter Ewald, is a method for computing long-range interactions (e.g. electrostatic interactions) in periodic systems. It was first developed as the method for calculating electrostatic energies of ionic crystals, a ...
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
Unix (; trademarked as UNIX) is a family of multitasking, multiuser computer operating systems that derive from the original AT&T Unix, whose development started in 1969 at the Bell Labs research center by Ken Thompson, Dennis Ritchie, and ot ...
and
Unix-like (
Linux
Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which in ...
) workstations, clusters of workstations, and on
Windows
Windows is a group of several Proprietary software, proprietary graphical user interface, graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, W ...
in sequential mode.
MDynaMix is developed at the Division of Physical Chemistry, Department of Materials and Environmental Chemistry,
Stockholm University
Stockholm University ( sv, Stockholms universitet) is a public research university in Stockholm, Sweden, founded as a college in 1878, with university status since 1960. With over 33,000 students at four different faculties: law, humanities, soci ...
, Sweden. It is released as
open-source software
Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Open ...
under a
GNU General Public License
The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses that guarantee end users the four freedoms to run, study, share, and modify the software. The license was the first copyleft for general us ...
(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
In thermodynamics, the chemical potential of a species is the energy that can be absorbed or released due to a change of the particle number of the given species, e.g. in a chemical reaction or phase transition. The chemical potential of a species ...
(is not parallelized)
* ''mge'' provides a
graphical user interface
The GUI ( "UI" by itself is still usually pronounced . or ), graphical user interface, is a form of user interface that allows User (computing), users to Human–computer interaction, interact with electronic devices through graphical icon (comp ...
to construct
molecular model
A molecular model is a physical model of an atomistic system that represents molecules and their processes. They play an important role in understanding chemistry and generating and testing hypotheses. The creation of mathematical models of molec ...
s and monitor dynamics process
Field of application
* Thermodynamic properties of liquids
*
Nucleic acid
Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main clas ...
- ions interaction
* Modeling of lipid bilayers
*
Polyelectrolyte
Polyelectrolytes are polymers whose repeating units bear an electrolyte group. Polycations and polyanions are polyelectrolytes. These groups dissociate in aqueous solutions (water), making the polymers charged. Polyelectrolyte properties are t ...
s
*
Ionic liquid
An ionic liquid (IL) is a salt in the liquid state. In some contexts, the term has been restricted to salts whose melting point is below a specific temperature, such as . While ordinary liquids such as water and gasoline are predominantly made of ...
s
* X-ray spectra of liquid water
*
Force Field development
See also
References
External links
* {{Official website, www.fos.su.se/~sasha/mdynamix
Ascalaph, graphical shell for MDynaMix(GNU GPL)
Molecular dynamics software
Free science software
Free software programmed in C++
Free software programmed in Fortran