"MPDyn" is a simulation program package to perform molecular simulations especially of macromolecular systems such as biological membrane, polymers, liquid crystals and so on. The following simulation techniques are available in the current version.
Various thermodynamics ensembles (NVE, NVT, NPT, NPnAT, NtT) are available using the above simulation techniques except for DPD, which generates only canonical ensemble. These molecular simulations can be applied to wide varieties of systems, including organic, inorganic materials, and metals. The source code of the "MPDyn" program was written in FORTRAN90 and was developed for the parallel MD by using MPI public library.
In order to ensure a long-time numerical stability of the MD trajectories, a time-reversible integrator constructed on the basis of the reversible RESPA (r-RESPA) algorithm was implemented. The non-Hamiltonian molecular dynamics techniques are used to generate the canonical or isothermal-isobaric ensembles, in which a set of equations of motions for additional degrees of freedom such as thermostats and barostat are also solved by r-RESPA. MD calculations of the system subjected to holonomic constraints can be undertaken by the SHAKE/RATTLE(/ROLL) procedure. Rigid-body dynamics is also available in this software. The simulation techniques to estimate free energy are also available (thermodynamic integration, cavity-based particle insertion). Some basic tools for the trajectory analysis are also provided.