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High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

I. Buch, M. J. Harvey, T. Giorgino, D. P. Anderson, G. De Fabritiis
Computational Biochemistry and Biophysics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/ Doctor Aiguader 88, 08003 Barcelona, Spain
Journal of Chemical Information and Modeling, Vol. 50, No. 3. (22 March 2010), pp. 397-403.

@article{buch2010high,

   title={High-throughput all-atom molecular dynamics simulations using distributed computing},

   author={Buch, I. and Harvey, MJ and Giorgino, T. and Anderson, DP and De Fabritiis, G.},

   journal={Journal of chemical information and modeling},

   volume={50},

   number={3},

   pages={397–403},

   issn={1549-9596},

   year={2010},

   publisher={ACS Publications}

}

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PMID: 20199097 Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU resources of nondedicated desktop and workstation computers. In particular, we demonstrate the capability of simulating thousands of all-atom molecular trajectories generated at an average of 20 ns/day each (for systems of ~30000-80000 atoms). In conjunction with a potential of mean force (PMF) protocol for computing binding free energies, we demonstrate the use of GPUGRID in the computation of accurate binding affinities of the Src SH2 domain/pYEEI ligand complex by reconstructing the PMF over 373 umbrella sampling windows of 55 ns each (20.5 micros of total data). We obtain a standard free energy of binding of -8.7
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