Implementation of Parallel Analyzes of Molecular Dynamics Simulation Trajectories

J. Štěpán¹, P. Kulhánek¹, N. K. Mishra¹, and J. Koča¹

¹National Centre for Biomolecular Research, Faculty of Science, Masaryk University,

Kotlářská 2, 611 37 Brno, e-mail: xstepan3@chemi.muni.cz

Molecular dynamics is widely used method of computational chemistry. With growing size of simulated systems and length of simulations, sequential analyzes of resulting trajectories become time demanding. Thus there is a need for tools that speed up trajectory processing and analyzes.

Recently, we have designed, implemented and tested tools for fast analyzes of long molecular simulation trajectories. Our implementation uses parallel processing of trajectories with arbitrary number of processors focused on binding free energy calculations. Moreover this approach can be easily extended to other analyzes, where analyzes of snapshots are independent on each other, e.g. radius of gyration, solute/solvent contacts, etc.

Developed tools were applied on the calculation of binding free energies using MM/PBSA method. Two biomolecular complexes were selected as a test case: a) LgtC galactosyltransferase from Niesseria meningitidis complexed with UDPGal and deoxylactose and b) lectin PA-IIL from Pseudomonas aeruginosa complexed with fucose. The 28-times acceleration on 32 processors was achieved, which shows 90 % parallel efficiency proving suitability of used approach.