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Title: Efficient approach to obtain free energy gradient using QM/MM MD simulation

The efficient computational approach denoted as charge and atom dipole response kernel (CDRK) model to consider polarization effects of the quantum mechanical (QM) region is described using the charge response and the atom dipole response kernels for free energy gradient (FEG) calculations in the quantum mechanical/molecular mechanical (QM/MM) method. CDRK model can reasonably reproduce energies and also energy gradients of QM and MM atoms obtained by expensive QM/MM calculations in a drastically reduced computational time. This model is applied on the acylation reaction in hydrated trypsin-BPTI complex to optimize the reaction path on the free energy surface by means of FEG and the nudged elastic band (NEB) method.
Authors:
;  [1] ;  [2] ;  [1]
  1. Department of Chemistry, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, Osaka 599-8531 (Japan)
  2. (RIMED), Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai 599-8531 (Japan)
Publication Date:
OSTI Identifier:
22499126
Resource Type:
Journal Article
Resource Relation:
Journal Name: AIP Conference Proceedings; Journal Volume: 1702; Journal Issue: 1; Conference: ICCMSE 2015: International conference of computational methods in sciences and engineering 2015, Athens (Greece), 20-23 Mar 2015; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; ACYLATION; ATOMS; DIPOLES; FREE ENERGY; KERNELS; POLARIZATION; QUANTUM MECHANICS; SIMULATION; SURFACES; TRYPSIN