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Normal mode analysis of macromolecular systems with the mobile block Hessian method

An Ghysels UGent, Veronique Van Speybroeck UGent, Dimitri Van Neck UGent, BR Brooks and Michel Waroquier UGent (2015) AIP Conference Proceedings. In AIP Conference Proceedings 1642. p.559-562
abstract
Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3N(a) x 3N(a) matrix with N-a the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each. Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible - but not necessarily optimized - geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian. In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example.
Please use this url to cite or link to this publication:
author
organization
year
type
conference (proceedingsPaper)
publication status
published
subject
keyword
partial optimization, NMA, reduced dimension, vibrational analysis, IR spectrum
in
AIP Conference Proceedings
series title
AIP Conference Proceedings
volume
1642
issue title
PROCEEDINGS OF THE INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2010 (ICCMSE-2010)
pages
559 - 562
publisher
AMER INST PHYSICS
conference name
International Conference of Computational Methods in Sciences and Engineering (ICCMSE)
conference location
Kos, Greece
conference start
2010-10-03
conference end
2010-10-08
Web of Science type
Proceedings Paper
Web of Science id
000354845400113
ISSN
0094-243X
ISBN
9780735412828
DOI
10.1063/14906742
language
English
UGent publication?
yes
classification
P1
copyright statement
I have transferred the copyright for this publication to the publisher
id
5991835
handle
http://hdl.handle.net/1854/LU-5991835
date created
2015-06-12 10:42:37
date last changed
2016-12-19 15:37:01
@inproceedings{5991835,
  abstract     = {Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3N(a) x 3N(a) matrix with N-a the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each.

Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible - but not necessarily optimized - geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian.

In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example.},
  author       = {Ghysels, An and Van Speybroeck, Veronique and Van Neck, Dimitri and Brooks, BR and Waroquier, Michel},
  booktitle    = {AIP Conference Proceedings},
  isbn         = {9780735412828},
  issn         = {0094-243X},
  keyword      = {partial optimization,NMA,reduced dimension,vibrational analysis,IR spectrum},
  language     = {eng},
  location     = {Kos, Greece},
  pages        = {559--562},
  publisher    = {AMER INST PHYSICS},
  title        = {Normal mode analysis of macromolecular systems with the mobile block Hessian method},
  url          = {http://dx.doi.org/10.1063/14906742},
  volume       = {1642},
  year         = {2015},
}

Chicago
Ghysels, An, Veronique Van Speybroeck, Dimitri Van Neck, BR Brooks, and Michel Waroquier. 2015. “Normal Mode Analysis of Macromolecular Systems with the Mobile Block Hessian Method.” In AIP Conference Proceedings, 1642:559–562. AMER INST PHYSICS.
APA
Ghysels, A., Van Speybroeck, V., Van Neck, D., Brooks, B., & Waroquier, M. (2015). Normal mode analysis of macromolecular systems with the mobile block Hessian method. AIP Conference Proceedings (Vol. 1642, pp. 559–562). Presented at the International Conference of Computational Methods in Sciences and Engineering (ICCMSE), AMER INST PHYSICS.
Vancouver
1.
Ghysels A, Van Speybroeck V, Van Neck D, Brooks B, Waroquier M. Normal mode analysis of macromolecular systems with the mobile block Hessian method. AIP Conference Proceedings. AMER INST PHYSICS; 2015. p. 559–62.
MLA
Ghysels, An, Veronique Van Speybroeck, Dimitri Van Neck, et al. “Normal Mode Analysis of Macromolecular Systems with the Mobile Block Hessian Method.” AIP Conference Proceedings. Vol. 1642. AMER INST PHYSICS, 2015. 559–562. Print.