Paper Citing NAMD - Abstract
Cickovski, Trevor; Sweet, Chris; Izaguirre, Jesus A.
MDL, a domain-specific language for molecular dynamics
40th Annual Simulation Symposium, Proceedings, 256-264, 2007
Molecular Dynamics (MD) involves solving Newton's equations of motion for a molecular system and propagating the system by time-dependent updates of atomic positions and velocities. As a severe limitation of molecular dynamics is the size of the timestep used for propagation, a key area of research is the development of efficient propagation algorithms which can maintain accuracy and stability with larger timesteps. We present MDL, an MD domain-specific language with the goals of allowing prototyping, testing and debugging of these algorithms. We illustrate the use of parallelism within MDL to implement the Finite Temperature String Method, and interfacing to visualization and graphical tools.
