Bioinformatics Molecular Dynamics

MDynaMix

Pinterest LinkedIn Tumblr

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. 

It has a code for simulations of mixtures of either rigid or flexible molecules, interacting by a force field consisting of Lennard Jones, electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a periodic rectangular, hexagonal or truncated octahedron cell. Rigid bonds are constrained by the SHAKE algorithm. A general purpose, scalable parallel molecular dynamics package for simulations of arbitrary mixtures of flexible or rigid molecules is presented. It allows use of most types of conventional molecular-mechanical force fields and contains a variety of auxiliary terms for inter and intramolecular interactions, including a harmonic bond-stretching. It can handle both isotropic and ordered systems. In case of flexible molecular models the double time step algorithm is used. Algorithms for NVE, NVT  and NpT statistical ensembles are used, as well as Ewald sum for treatment of the electrostatic interactions. Treatment of quantum correction to the atomic motion can be done within the path integral molecular dynamics approach. Package works on Unix/Linux workstations and clusters of workstations as well as 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).

Features 

  • Thermodynamic properties of liquids
  • Nucleic acid – ions interaction
  • Modeling of lipid bilayers
  • Polyelectrolytes
  • Ionic liquids 
  • X-ray spectra of liquid water
  • Force Field development 

The simulation cell can be either cubic, rectangular, hexagonal or a truncated octahedron, with corresponding periodic boundary conditions and minimum images. In all cases, the optimized Ewald method can be used to treat the Coulombic interactions. Double time-step or constrained dynamics schemes are included. An external electric field can be used across the simulation cell. The whole program is highly modular and is written in standard Fortran. It can be compiled to run efficiently both on parallel and sequential computers. The inherent complexity of the studied system does not affect the scalability of the program. The scaling is good with the size of the system and with the number of processors. The portability of the program is good, it runs regularly on many common single- and multiprocessor platforms, both scalar and vector architectures included.

The program can be run both in sequential and parallel execution. The parallel version uses a “replicated data” strategy. It can be run on any parallel architecture or workstation cluster with the MPI that should be parallel to the environment installed. Utilities for preparation of molecular description files and for trajectory analysis are included in this simulation tool.

Write A Comment