Molecular Dynamics of Mixtures (MDynaMix) is a computer
software
Software consists of computer programs that instruct the Execution (computing), execution of a computer. Software also includes design documents and specifications.
The history of software is closely tied to the development of digital comput ...
package for general purpose
molecular dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), 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 dynamics ( ...
to simulate mixtures of molecules, interacting by
AMBER
Amber is fossilized tree resin. Examples of it have been appreciated for its color and natural beauty since the Neolithic times, and worked as a gemstone since antiquity."Amber" (2004). In Maxine N. Lurie and Marc Mappen (eds.) ''Encyclopedia ...
- 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 CH ...
-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 mod ...
.
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 the electrostatic energies of ionic crys ...
to treat electrostatic interactions.
The code was written in a mix of
Fortran 77 and 90 (with
Message Passing Interface
The Message Passing Interface (MPI) is a portable message-passing standard designed to function on parallel computing architectures. The MPI standard defines the syntax and semantics of library routines that are useful to a wide range of use ...
(MPI) for parallel execution). The package runs on
Unix
Unix (, ; trademarked as UNIX) is a family of multitasking, multi-user 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, a ...
and
Unix-like
A Unix-like (sometimes referred to as UN*X, *nix or *NIX) operating system is one that behaves in a manner similar to a Unix system, although not necessarily conforming to or being certified to any version of the Single UNIX Specification. A Uni ...
(
Linux
Linux ( ) is a family of open source Unix-like operating systems based on the Linux kernel, an kernel (operating system), operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically package manager, pac ...
) workstations, clusters of workstations, and on
Windows
Windows is a Product lining, product line of Proprietary software, proprietary graphical user interface, graphical operating systems developed and marketed by Microsoft. It is grouped into families and subfamilies that cater to particular sec ...
in sequential mode.
MDynaMix is developed at the Division of Physical Chemistry, Department of Materials and Environmental Chemistry,
Stockholm University
Stockholm University (SU) () is a public university, 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, social ...
, Sweden. It is released as
open-source software
Open-source software (OSS) is Software, computer software that is released under a Open-source license, license in which the copyright holder grants users the rights to use, study, change, and Software distribution, distribute the software an ...
under a
GNU General Public License
The GNU General Public Licenses (GNU GPL or simply GPL) are a series of widely used free software licenses, or ''copyleft'' licenses, that guarantee end users the freedom to run, study, share, or modify the software. The GPL was the first ...
(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 Chemical specie, 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 potent ...
(is not parallelized)
* ''mge'' provides a
graphical user interface
A graphical user interface, or GUI, is a form of user interface that allows user (computing), users to human–computer interaction, interact with electronic devices through Graphics, graphical icon (computing), icons and visual indicators such ...
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 mole ...
s and monitor dynamics process
Field of application
* Thermodynamic properties of liquids
*
Nucleic acid
Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nuclei ...
- 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 (chemistry), salt in the liquid state at ambient conditions. 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 wate ...
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