Multiple active zones in hybrid QM/MM molecular dynamics simulations for large biomolecular systems

Physical Chemistry Chemical Physics : PCCP
Juan Torras

Abstract

A new QM/MM molecular dynamics approach that can deal with the dynamics of large real systems involving several simultaneous active zones is presented. Multiple, unconnected but interacting quantum regions are treated independently in an ordinary QM/MM approach but in a manner which converges to a unique simulation. The multiple active zones in the hybrid QM/MM molecular dynamics methodology (maz-QM/MM MD) involve molecular dynamics that is driving the whole simulation with several parallel executions of energy gradients within the QM/MM approach that merge into each MD step. The Ewald-summation method is used to incorporate long-range electrostatic interactions among the active zones in conjunction with periodic boundary conditions. To illustrate and ascertain capabilities and limitations, we present several benchmark calculations using this approach. Our results show that the maz-QM/MM MD method is able to provide simultaneous treatment of several active zones of very large proteins such as the Cu-4His-ΔC* cage, a self-assembly of a 24-mer cage-like protein ferritin.

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Citations

May 25, 2016·Physical Chemistry Chemical Physics : PCCP·Yoshio Nishimoto, Dmitri G Fedorov
Sep 20, 2016·Journal of Chemical Theory and Computation·Jorge Soto-DelgadoJuan Torras
Jan 24, 2017·Journal of Computational Chemistry·Yoshio Nishimoto, Dmitri G Fedorov
Feb 9, 2018·Chemical Communications : Chem Comm·Juan Torras, Carlos Alemán

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