Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions

Abstract

A massively parallel program for quantum mechanical‐molecular mechanical (QM/MM) molecular dynamics simulation, called Platypus (PLATform for dYnamic Protein Unified Simulation), was developed to elucidate protein functions. The speedup and the parallelization ratio of Platypus in the QM and QM/MM calculations were assessed for a bacteriochlorophyll dimer in the photosynthetic reaction center (DIMER) on the K computer, a massively parallel computer achieving 10 PetaFLOPs with 705,024 cores. Platypus exhibited the increase in speedup up to 20,000 core processors at the HF/cc‐pVDZ and B3LYP/cc‐pVDZ, and up to 10,000 core processors by the CASCI(16,16)/6‐31G** calculations. We also performed excited QM/MM‐MD simulations on the chromophore of Sirius (SIRIUS) in water. Sirius is a pH‐insensitive and photo‐stable ultramarine fluorescent protein. Platypus accelerated on‐the‐fly excited‐state QM/MM‐MD simulations for SIRIUS in water, using over 4000 core processors. In addition, it also succeeded in 50‐ps (200,000‐step) on‐the‐fly excited‐state QM/MM‐MD simulations for the SIRIUS in water. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Multistructural microiteration combined with QM/MM-ONIOM electrostatic embedding

“…QM/ MM methods are now available in many ab initio quantum chemistry calculation programs. [16][17][18][19][20][21] Moreover, many ab initio quantum chemistry calculation programs [22][23][24] and molecular dynamics (MD) simulation programs [25][26][27][28][29][30][31][32] have an interface that performs a QM/MM calculation in cooperation with the other program.…”

Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations

“… 80 Other QM/MM-MD programs are also found in the literature: NAMD, 81 , 82 Dynamo, 83 , 84 etc. In addition, QM/MM calculations are available in electronic structure programs (Gaussian, 85 Q-Chem, 86 deMon2k, 87 Platypus, 88 etc.) and by interface programs (ChemShell 89 and PUPIL 90 ).…”