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MDLab: A molecular dynamics simulation prototyping environment

Trevor Cickovski, Santanu Chatterjee, Jacob Wenger, Christopher R. Sweet, Jesus A. Izaguirre
Natural Sciences Collegium, Eckerd College, 115 Sheen Science C, St. Petersburg, FL 33711, USA
Journal of Computational Chemistry, Vol. 31, No. 7. (30 October 2010), pp. 1345-1356.

@article{cickovski2010mdlab,

   title={MDLab: A molecular dynamics simulation prototyping environment},

   author={Cickovski, T. and Chatterjee, S. and Wenger, J. and Sweet, C.R. and Izaguirre, J.A.},

   journal={Journal of Computational Chemistry},

   volume={31},

   number={7},

   pages={1345–1356},

   issn={1096-987X},

   year={2010},

   publisher={John Wiley & Sons}

}

Molecular dynamics (MD) simulation involves solving Newton’s equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep Deltat. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly string method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net.
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