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Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach

An Ghysels UGent, Dimitri Van Neck UGent, Bernard R. Brooks, Veronique Van Speybroeck UGent and Michel Waroquier UGent (2009) JOURNAL OF CHEMICAL PHYSICS. 130(8).
abstract
In a previous paper [Ghysels , J. Chem. Phys. 126, 224102 (2007)] the mobile block Hessian (MBH) approach was presented. The method was designed to accurately compute vibrational modes of partially optimized molecular structures. The key concept was the introduction of several blocks of atoms, which can move as rigid bodies with respect to a local, fully optimized subsystem. The choice of the blocks was restricted in the sense that none of them could be connected, and also linear blocks were not taken into consideration. In this paper an extended version of the MBH method is presented that is generally applicable and allows blocks to be adjoined by one or two common atoms. This extension to all possible block partitions of the molecule provides a structural flexibility varying from very rigid to extremely relaxed. The general MBH method is very well suited to study selected normal modes of large macromolecules (such as proteins and polymers) because the number of degrees of freedom can be greatly reduced while still keeping the essential motions of the molecular system. The reduction in the number of degrees of freedom due to the block linkages is imposed here directly using a constraint method, in contrast to restraint methods where stiff harmonic couplings are introduced to restrain the relative motion of the blocks. The computational cost of this constraint method is less than that of an implementation using a restraint method. This is illustrated for the alpha-helix conformation of an alanine-20-polypeptide.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
macromolecules, polymers, molecular configurations, proteins, vibrational states
journal title
JOURNAL OF CHEMICAL PHYSICS
J. Chem. Phys.
volume
130
issue
8
pages
084107 -
publisher
Amer. Inst. Physics
place of publication
Melville, USA
Web of Science type
Article
Web of Science id
000263804200012
JCR category
PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
JCR impact factor
3.093 (2009)
JCR rank
6/33 (2009)
JCR quartile
1 (2009)
ISSN
0021-9606
DOI
10.1063/1.3071261
language
English
UGent publication?
yes
classification
A1
additional info
A.G. is Aspirant of the Fund for Scientific Research-Flanders (FWO). This work is supported by the Fund for Scientific Research-Flanders (FWO) and by the Research Board of Ghent University (BOF).
id
519510
handle
http://hdl.handle.net/1854/LU-519510
date created
2009-03-16 16:22:42
date last changed
2009-03-17 16:19:03
@article{519510,
  abstract     = {In a previous paper [Ghysels , J. Chem. Phys. 126, 224102 (2007)] the mobile block Hessian (MBH) approach was presented. The method was designed to accurately compute vibrational modes of partially optimized molecular structures. The key concept was the introduction of several blocks of atoms, which can move as rigid bodies with respect to a local, fully optimized subsystem. The choice of the blocks was restricted in the sense that none of them could be connected, and also linear blocks were not taken into consideration. In this paper an extended version of the MBH method is presented that is generally applicable and allows blocks to be adjoined by one or two common atoms. This extension to all possible block partitions of the molecule provides a structural flexibility varying from very rigid to extremely relaxed. The general MBH method is very well suited to study selected normal modes of large macromolecules (such as proteins and polymers) because the number of degrees of freedom can be greatly reduced while still keeping the essential motions of the molecular system. The reduction in the number of degrees of freedom due to the block linkages is imposed here directly using a constraint method, in contrast to restraint methods where stiff harmonic couplings are introduced to restrain the relative motion of the blocks. The computational cost of this constraint method is less than that of an implementation using a restraint method. This is illustrated for the alpha-helix conformation of an alanine-20-polypeptide.},
  author       = {Ghysels, An and Van Neck, Dimitri and Brooks, Bernard R. and Van Speybroeck, Veronique and Waroquier, Michel},
  issn         = {0021-9606},
  journal      = {JOURNAL OF CHEMICAL PHYSICS},
  keyword      = {macromolecules,polymers,molecular configurations,proteins,vibrational states},
  language     = {eng},
  number       = {8},
  publisher    = {Amer. Inst. Physics},
  title        = {Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach},
  url          = {http://dx.doi.org/10.1063/1.3071261},
  volume       = {130},
  year         = {2009},
}

Chicago
Ghysels, An, Dimitri Van Neck, Bernard R. Brooks, Veronique Van Speybroeck, and Michel Waroquier. 2009. “Normal Modes for Large Molecules with Arbitrary Link Constraints in the Mobile Block Hessian Approach.” Journal of Chemical Physics 130 (8): 084107.
APA
Ghysels, A., Van Neck, D., Brooks, B. R., Van Speybroeck, V., & Waroquier, M. (2009). Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach. JOURNAL OF CHEMICAL PHYSICS, 130(8), 084107.
Vancouver
1.
Ghysels A, Van Neck D, Brooks BR, Van Speybroeck V, Waroquier M. Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach. JOURNAL OF CHEMICAL PHYSICS. Melville, USA: Amer. Inst. Physics; 2009;130(8):084107.
MLA
Ghysels, An, Dimitri Van Neck, Bernard R. Brooks, et al. “Normal Modes for Large Molecules with Arbitrary Link Constraints in the Mobile Block Hessian Approach.” JOURNAL OF CHEMICAL PHYSICS 130.8 (2009): 084107. Print.