The Molecular Dynamics Language (MDL) provides a high-level Python interface for molecular dynamics, enabling customizable simulations including importable modules, new integrator prototyping, and force algorithm addition and testing.
The Molecular Dynamics Language (MDL) is intended to allow users to represent molecular dynamics (MD) simulations at a high level. This includes the ability to interact directly with running simulations and prototype new integration schemes using several different methods, including both objects and functions which update position and velocity sets. The language builds upon Python and uses a set of SWIG-wrapped libraries from the software framework ProtoMol, developed in part to meet the heavy performance requirements of long-range force computations. Adding and testing new force evaluation algorithms are helped through the modular design of MDL, as well as new simulation protocols. The API includes functionality to access simulation data, input and output data in different files and formats, add data plots, add different types of forces to individual integrators, use existing integrators from the ProtoMol framework in Python, and convert data vectors into fast Numeric arrays. MDL is currently available for 32-bit Linux and Mac OS X.
May 4, 2016