Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules.

Abstract : We propose a rigorous method for removing rigid-body motions from a given molecular dynamics trajectory of a flexible macromolecule. The method becomes exact in the limit of an infinitesimally small sampling step for the input trajectory. In a recent paper [G. Kneller, J. Chem. Phys. 128, 194101 (2008)], one of us showed that virtual internal atomic displacements for small time increments can be derived from Gauss' principle of least constraint, which leads to a rotational superposition problem for the atomic coordinates in two consecutive time frames of the input trajectory. Here, we demonstrate that the accumulation of these displacements in a molecular-fixed frame, which evolves in time according to the virtual rigid-body motions, leads to the desired trajectory for internal motions. The atomic coordinates in the input and output trajectory are related by a roto-translation, which guarantees that the internal energy of the molecule is left invariant. We present a convenient implementation of our method, in which the accumulation of the internal displacements is performed implicitly. Two numerical examples illustrate the difference to the classical approach for removing macromolecular rigid-body motions, which consists of aligning its configurations in the input trajectory with a fixed reference structure.
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https://hal.archives-ouvertes.fr/hal-00720598
Contributor : Isabelle Frapart <>
Submitted on : Wednesday, July 25, 2012 - 10:39:58 AM
Last modification on : Tuesday, June 18, 2019 - 11:46:02 AM

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Guillaume Chevrot, Paolo Calligari, Konrad Hinsen, Gerald R Kneller. Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules.. Journal of Chemical Physics, American Institute of Physics, 2011, 135 (8), pp.084110. ⟨10.1063/1.3626275⟩. ⟨hal-00720598⟩

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