.. Dash documentation master file, created by sphinx-quickstart on Tue Apr 25 15:12:44 2017. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Welcome to DASH's documentation! ================================ DASH is a GPU-accelerated molecular dynamics software package designed for both atomistic and coarse grained simulations. DASH is controlled via a powerful python interface, which gives the user full control to set up, modify, and analyze simulations all within one script. Using efficient parallel algorithms, DASH also provides the facility to compute arbitrarly complex user-defined types of data while maintaining high performance. DASH is specifically optimized for running with the the advanced sampling package SSAGES, allowing up to double the performance of leading competitors. With plain molecule dynamics, performance in DASH for simple molecular dynamics is comparable to the fastest codes available. DASH supports several water models including TIP3P, TIP4P (and variants), as well as the E3B model, a fast and robust 3-body water model parameterized to capture much of the water phase diagram (Kumar, JPC, 2008). In addition to these features, DASH provides all the standard functionality users have come to expect from a batteries-included molecules dynamics package, including a variety of thermostats, barostats, elegant methods for dealing with molecules, long range charge computation, multiple force fields, and much more. .. DASH uses the SETTLE algorithm (Miyamoto, JCC, 1992) to efficiently model water molecules. In addition to standard water potentials such as TIP3P, TIP4P and similar, DASH includes the new E3B water model (Tainter, JCP, 2011), which has been parameterized to accurately capture much of the water phase diagram. Getting started .. toctree:: :maxdepth: 1 compiling getting-started Core functionality .. toctree:: :maxdepth: 2 state data-recording writing-trajectories reading-trajectories Atoms Bounds Units python-operation molecule Potentials .. toctree:: :maxdepth: 2 fix-bond-harmonic fix-bond-fene fix-angle-harmonic fix-angle-charmm fix-angle-cosinedelta fix-dihedral-opls fix-dihedral-charmm fix-pair-LJ fix-pair-LJFS fix-pair-TICG fix-charge-DSF fix-charge-Ewald fix-wall-LJ126 fix-wall-harmonic External potentials: .. toctree:: :maxdepth: 2 fix-external-harmonic fix-external-quartic springs Thermostats and Barostats: .. toctree:: :maxdepth: 2 fix-NoseHoover fix-pressure-Berendsen fix-Langevin fix-NVT-Andersen fix-NVT-rescale Integrators: .. toctree:: :maxdepth: 2 integrator-Verlet integrator-relax Utilities and external functionality .. toctree:: :maxdepth: 2 lammps-reader ssages Indices and tables ================== * :ref:`search`