A domain decomposition molecular dynamics program for the simulation of flexible molecules of spherically-symmetrical and nonspherical sites. II. Extension to NVT and NPT ensembles Original Research Article

We describe the algorithms for NVT and NPT-ensemble simulations developed within the parallel molecular dynamics program GBMOLDD. This program uses the domain decomposition algorithm and is targeted at large-scale simulations of molecular systems (particularly polymers and liquid crystals) composed of both spherically-symmetric and nonspherical sites. The nonspherical sites can be described either by a Gay–Berne potential or by soft repulsive spherocylinders. The molecules can be of arbitrary topology and the intramolecular forces are described via standard force fields. We tested the stability of both leap-frog and velocity-Verlet integrators on two “real-life” systems—a nematic liquid crystal phase of 1944 one-site Gay–Berne molecules and on 512 flexible liquid-crystalline dimers. In both cases the algorithm demonstrates good stability over the typical simulation times required for new phase formation and/or molecular relaxation processes.