MDynaMix
is a general purpose molecular dynamics

Molecular dynamics

Molecular dynamics is a computer simulation of physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms...

 software package for simulations mixtures of molecules,
interacting by AMBER

AMBER

AMBER is a family of force fields for molecular dynamics of biomolecules originally developed by the late Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields...

/CHARMM

CHARMM

CHARMM is the name of a widely used set of force fields for molecular dynamics as well as the name for the molecular dynamics simulation and analysis package associated with them...

 like force fields

Force field (chemistry)

In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles . Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical...

 in a periodic boundary conditions

Periodic boundary conditions

In mathematical models and computer simulations, periodic boundary conditions are a set of boundary conditions that are often used to simulate a large system by modelling a small part that is far from its edge...

.
MDynaMix is developed at the Stockholm University, Sweden.
Algorithms for NVE, NVT, NPT and anisotropic NPT ensembles are employed, as well as Ewald summation

Ewald summation

Ewald summation, named after Paul Peter Ewald, is a method for computing the interaction energies of periodic systems , particularly electrostatic energies. Ewald summation is a special case of the Poisson summation formula, replacing the summation of interaction energies in real space with an...

 for treatment of the electrostatic interactions.
The code was written in Fortran 77 (with MPI

Message Passing Interface

Message Passing Interface is a standardized and portable message-passing system designed by a group of researchers from academia and industry to function on a wide variety of parallel computers...

 for parallel execution) and C++

C++

C++ is a statically typed, free-form, multi-paradigm, compiled, general-purpose programming language. It is regarded as an intermediate-level language, as it comprises a combination of both high-level and low-level language features. It was developed by Bjarne Stroustrup starting in 1979 at Bell...

 and released under the GNU GPL. 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
  Force field (chemistry)
  In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles . Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical...
  
  
• 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
  Thermodynamic free energy
  The thermodynamic free energy is the amount of work that a thermodynamic system can perform. The concept is useful in the thermodynamics of chemical or thermal processes in engineering and science. The free energy is the internal energy of a system less the amount of energy that cannot be used to...
  
  / chemical potential
  Chemical potential
  Chemical potential, symbolized by μ, is a measure first described by the American engineer, chemist and mathematical physicist Josiah Willard Gibbs. It is the potential that a substance has to produce in order to alter a system...
  
   (is not parallelized)
• mge provides graphical interface for molecular model
  Molecular model
  A molecular model, in this article, is a physical model that represents molecules and their processes. The creation of mathematical models of molecular properties and behaviour is molecular modelling, and their graphical depiction is molecular graphics, but these topics are closely linked and each...
  
  s construction and monitoring of dynamics process

Field of application

• Thermodynamic properties of liquids
• Nucleic acid
  Nucleic acid
  Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...
  
   - ions interaction
• Modeling of lipid bilayers
• Polyelectrolyte
  Polyelectrolyte
  Polyelectrolytes are polymers whose repeating units bear an electrolyte group. These groups will dissociate in aqueous solutions , making the polymers charged. Polyelectrolyte properties are thus similar to both electrolytes and polymers , and are sometimes called polysalts. Like salts, their...
  
  s
• Ionic liquid
  Ionic liquid
  An ionic liquid is a salt in the liquid state. In some contexts, the term has been restricted to salts whose melting point is below some arbitrary temperature, such as . While ordinary liquids such as water and gasoline are predominantly made of electrically neutral molecules, ILs are largely made...
  
  s
• X-ray spectra of liquid water
• Force Field
  Force field (chemistry)
  In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles . Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical...
  
   development

See also

External links

• Home page
• Graphical shell for MDynaMix