### Abstract

Vibrational spectra of proteins potentially give insight into biologically significant molecular motion and the proportions of different types of secondary structure. Vibrational spectra can be calculated either from normal modes obtained by diagonalizing the mass-weighted Hessian or from the time autocorrelation function derived from molecular dynamics trajectories. The Hessian matrix is calculated from force fields because it is not practical to calculate the Hessian from quantum mechanics for large molecules. As an alternative to molecular dynamics the spectral response can be calculated from a time autocorrelation derived from numerical solution of the harmonic equations of motion, resulting in calculations at least 4 times faster. Because the calculation also scales linearly with number of atoms, N, it is faster than normal-mode calculations that scale as N^{3} for proteins with more then 4,700 atoms. Using this method it is practical to perform all-atom calculations for large biological systems, for example viral capsids, with the order of 10^{5} atoms.

Original language | English (US) |
---|---|

Pages (from-to) | 795-801 |

Number of pages | 7 |

Journal | European Biophysics Journal |

Volume | 42 |

Issue number | 11-12 |

DOIs | |

State | Published - Dec 2013 |

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### Keywords

- Equation of motion
- Infrared
- Macromolecules
- Molecular dynamics
- Proteins

### ASJC Scopus subject areas

- Biophysics

### Cite this

*European Biophysics Journal*,

*42*(11-12), 795-801. https://doi.org/10.1007/s00249-013-0927-8

**Fast calculation of the infrared spectra of large biomolecules.** / Mott, A. J.; Thirumuruganandham, S. P.; Thorpe, Michael; Rez, Peter.

Research output: Contribution to journal › Article

*European Biophysics Journal*, vol. 42, no. 11-12, pp. 795-801. https://doi.org/10.1007/s00249-013-0927-8

}

TY - JOUR

T1 - Fast calculation of the infrared spectra of large biomolecules

AU - Mott, A. J.

AU - Thirumuruganandham, S. P.

AU - Thorpe, Michael

AU - Rez, Peter

PY - 2013/12

Y1 - 2013/12

N2 - Vibrational spectra of proteins potentially give insight into biologically significant molecular motion and the proportions of different types of secondary structure. Vibrational spectra can be calculated either from normal modes obtained by diagonalizing the mass-weighted Hessian or from the time autocorrelation function derived from molecular dynamics trajectories. The Hessian matrix is calculated from force fields because it is not practical to calculate the Hessian from quantum mechanics for large molecules. As an alternative to molecular dynamics the spectral response can be calculated from a time autocorrelation derived from numerical solution of the harmonic equations of motion, resulting in calculations at least 4 times faster. Because the calculation also scales linearly with number of atoms, N, it is faster than normal-mode calculations that scale as N3 for proteins with more then 4,700 atoms. Using this method it is practical to perform all-atom calculations for large biological systems, for example viral capsids, with the order of 105 atoms.

AB - Vibrational spectra of proteins potentially give insight into biologically significant molecular motion and the proportions of different types of secondary structure. Vibrational spectra can be calculated either from normal modes obtained by diagonalizing the mass-weighted Hessian or from the time autocorrelation function derived from molecular dynamics trajectories. The Hessian matrix is calculated from force fields because it is not practical to calculate the Hessian from quantum mechanics for large molecules. As an alternative to molecular dynamics the spectral response can be calculated from a time autocorrelation derived from numerical solution of the harmonic equations of motion, resulting in calculations at least 4 times faster. Because the calculation also scales linearly with number of atoms, N, it is faster than normal-mode calculations that scale as N3 for proteins with more then 4,700 atoms. Using this method it is practical to perform all-atom calculations for large biological systems, for example viral capsids, with the order of 105 atoms.

KW - Equation of motion

KW - Infrared

KW - Macromolecules

KW - Molecular dynamics

KW - Proteins

UR - http://www.scopus.com/inward/record.url?scp=84896715805&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84896715805&partnerID=8YFLogxK

U2 - 10.1007/s00249-013-0927-8

DO - 10.1007/s00249-013-0927-8

M3 - Article

C2 - 24037120

AN - SCOPUS:84896715805

VL - 42

SP - 795

EP - 801

JO - European Biophysics Journal

JF - European Biophysics Journal

SN - 0175-7571

IS - 11-12

ER -