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Efficient calculation of QM/MM frequencies with the mobile block hessian

An Ghysels UGent, H Lee III Woodcock, Joseph D Larkin, Benjamin T Miller, Yihan Shao, Jing Kong, Dimitri Van Neck UGent, Veronique Van Speybroeck UGent, Michel Waroquier UGent and Bernard R Brooks (2011) JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 7(2). p.496-514
abstract
The calculation of the analytical second derivative matrix (Hessian) is the bottleneck for vibrational analysis in QM/MM systems when an electrostatic embedding scheme is employed. Even with a small number of QM atoms in the system, the presence of MM atoms increases the computational cost dramatically: the long-range Coulomb interactions require that additional coupled perturbed self-consistent field (CPSCF) equations need to be solved for each MM atom displacement. This paper presents an extension to the Mobile Block Hessian (MBH) formalism for QM/MM calculations with blocks in the MM region and its implementation in a parallel version of the Q-Chem/CHARMM interface. MBH reduces both the CPU time and the memory requirements compared to the standard full Hessian QM/MM analysis, without the need to use a cutoff distance for the electrostatic interactions. Special attention is given to the treatment of link atoms which are usually present when the QM/MM border cuts through a covalent bond. Computational efficiency improvements are highlighted using a reduced chorismate mutase enzyme system, consisting of 24 QM atoms and 306 MM atoms, as a test example. In addition, the drug bortezomib, used for cancer treatment of myeloma, has been studied as a test case with multiple MBH block choices and both a QM and QM/MM description. The accuracy of the calculated Hessians is quantified by imposing Eckart constraints, which allows for the assessment of numerical errors in second derivative procedures. The results show that MBH within the QM/MM description not only is a computationally attractive method but also produces accurate results.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
journal title
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
J. chem. theory comput.
volume
7
issue
2
pages
496 - 514
Web of Science type
Article
Web of Science id
000287049200023
JCR category
PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
JCR impact factor
5.215 (2011)
JCR rank
2/32 (2011)
JCR quartile
1 (2011)
ISSN
1549-9618
DOI
10.1021/ct100473f
project
HPC-UGent: the central High Performance Computing infrastructure of Ghent University
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1182113
handle
http://hdl.handle.net/1854/LU-1182113
date created
2011-03-04 10:58:31
date last changed
2013-09-17 10:46:19
@article{1182113,
  abstract     = {The calculation of the analytical second derivative matrix (Hessian) is the bottleneck for vibrational analysis in QM/MM systems when an electrostatic embedding scheme is employed. Even with a small number of QM atoms in the system, the presence of MM atoms increases the computational cost dramatically: the long-range Coulomb interactions require that additional coupled perturbed self-consistent field (CPSCF) equations need to be solved for each MM atom displacement. This paper presents an extension to the Mobile Block Hessian (MBH) formalism for QM/MM calculations with blocks in the MM region and its implementation in a parallel version of the Q-Chem/CHARMM interface. MBH reduces both the CPU time and the memory requirements compared to the standard full Hessian QM/MM analysis, without the need to use a cutoff distance for the electrostatic interactions. Special attention is given to the treatment of link atoms which are usually present when the QM/MM border cuts through a covalent bond. Computational efficiency improvements are highlighted using a reduced chorismate mutase enzyme system, consisting of 24 QM atoms and 306 MM atoms, as a test example. In addition, the drug bortezomib, used for cancer treatment of myeloma, has been studied as a test case with multiple MBH block choices and both a QM and QM/MM description. The accuracy of the calculated Hessians is quantified by imposing Eckart constraints, which allows for the assessment of numerical errors in second derivative procedures. The results show that MBH within the QM/MM description not only is a computationally attractive method but also produces accurate results.},
  author       = {Ghysels, An and Woodcock, H Lee III and Larkin, Joseph D and Miller, Benjamin T and Shao, Yihan and Kong, Jing and Van Neck, Dimitri and Van Speybroeck, Veronique and Waroquier, Michel and Brooks, Bernard R},
  issn         = {1549-9618},
  journal      = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION},
  language     = {eng},
  number       = {2},
  pages        = {496--514},
  title        = {Efficient calculation of QM/MM frequencies with the mobile block hessian},
  url          = {http://dx.doi.org/10.1021/ct100473f},
  volume       = {7},
  year         = {2011},
}

Chicago
Ghysels, An, H Lee III Woodcock, Joseph D Larkin, Benjamin T Miller, Yihan Shao, Jing Kong, Dimitri Van Neck, Veronique Van Speybroeck, Michel Waroquier, and Bernard R Brooks. 2011. “Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian.” Journal of Chemical Theory and Computation 7 (2): 496–514.
APA
Ghysels, A., Woodcock, H. L. I., Larkin, J. D., Miller, B. T., Shao, Y., Kong, J., Van Neck, D., et al. (2011). Efficient calculation of QM/MM frequencies with the mobile block hessian. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7(2), 496–514.
Vancouver
1.
Ghysels A, Woodcock HLI, Larkin JD, Miller BT, Shao Y, Kong J, et al. Efficient calculation of QM/MM frequencies with the mobile block hessian. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2011;7(2):496–514.
MLA
Ghysels, An, H Lee III Woodcock, Joseph D Larkin, et al. “Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian.” JOURNAL OF CHEMICAL THEORY AND COMPUTATION 7.2 (2011): 496–514. Print.