science/mdynamix 5.3.0_1 FreeBSD

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.