Computational Modeling and Simulations
Nikolay Simakov 

pDynamo: hybrid quantum chemical (QC) / molecular mechanical simulations

pDynamo is an open-source molecular simulation program for bimolecular modeling , for example, modeling of enzymatic reactions, using hybrid quantum chemical/molecular mechanical approach. My contribution is optimization and parallelization (OpenMP/MPI) of the existing serial code. In comparison with the original serial code, the optimizations have resulted in overall 5 times acceleration. The implemented parallel version has linear scaling for cross-grain parallelization (used in Umbrella sampling), and about 2 times acceleration for fine-grain parallelization (this is achieved with only part of the code being optimized/parallelized and the rest is still in the process).The changes are not yet released, for other pDynamo capabilities see www.pdynamo.org.