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Introduction

MDynaMix is a general purpose molecular dynamics code for simulations of mixtures of rigid or flexible molecules, interacting by standard molecular-mechanics force field including electrostatic and Lennard-Jones potentials for electrostatic interactions as well as terms describing covalent bonds, angles and dihedral angles. The program is well suited for simulations of flexible molecules based on the double time step algorithm. Alternatively, rigid bonds can be treated by the SHAKE algorithm. Algorithms for NVE, NVT, NPT and anisotropic NPT ensembles are implemented. The long-range electrostatic interactions are treated by the Ewald summation method, or alternatively by a reation field or simple cutoff. The program can be run both in sequential and parallel execution, in the latter case the MPI parallel environment is required. From v.5.1 possibility for taking into account quantum motion of nuclei using Path Integral approach is implemented. Expanded ensemble mode of simulations for calculation of solvation free energies is added in v.5.2.

The program is written in standard Fortran 77/90 and thus can be run on any computer system having a Fortran compiler.

The program is originally based on the MOLDYN program by Aatto Laaksonen, available from the CCP5 program library, Daresbury Lab, UK. Since 1993 many additional changes were made by Alexander Lyubartsev. The first parallelized version of the program (v.4.0) was published in:

A.P.Lyubartsev, A.Laaksonen, ``MDynaMix - a scalable portable parallel MD simulation package for arbitrary molecular mixtures" Computer Physics Communications, v.128(3), pp.565-589 (2000)

Apart the main MDynaMix block, the package includes the following components:



Subsections
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Next: Changes from previous versions Up: MDynaMix Package version 5.2.7 Previous: Contents   Contents
Alexander Lyubartsev 2015-02-06