Applications of High Performance Computing: Born–Oppenheimer Molecular Dynamics of Complex Formation in Aqueous Solutions

Maria G. Khrenova; Dmitry P. Kapusta; Ilya V. Babchuk; Yulia I. Meteleshko

doi:10.14529/jsfi180312

Authors

Maria G. Khrenova Lomonosov Moscow State University, Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences
Dmitry P. Kapusta Lomonosov Moscow State University
Ilya V. Babchuk Lomonosov Moscow State University
Yulia I. Meteleshko Lomonosov Moscow State University

DOI:

https://doi.org/10.14529/jsfi180312

Abstract

The progress of supercomputer technologies initiated the development of methods of computational chemistry and their applications, particularly molecular dynamic simulations with ab initio potentials. These new methods allow to solve important problems of chemistry and technology. Particularly, solvent extraction and separation techniques are widely used to decrease the amount of radioactive wastes, especially radioactive caesium isotopes present in liquid phases. We demonstrated that the calculated binding constants between the alkali cation and calix[4]arene differ 103 times for Cs+ and Na+ ions, that is in good agreement with the experimental value. We report the results of benchmark calculations of our model system composed of 929 atoms described in the density functional theory approximation with the GGA-type functional PBE with the empirical dispersion correction D3 and combined basis of Gaussian functions and plane waves DZVP with Goedecker-Teter-Hutter pseudopotentials. We demonstrate that efficiency of calculations decrease to about half if the amount of nodes is 16 on the Lomonosov-2 supercomputer.

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