title: 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.
authors: Centre de Biophys. Moléculaire, CNRS, Rue Charles Sadron, 45071 Orléans, France.
authors: Guillaume
authors: G
authors: Chevrot
authors: Paolo
authors: P
authors: Calligari
authors: Konrad
authors: K
authors: Hinsen
authors: Gerald R
authors: GR
authors: Kneller
mesh_terms: D008962:Models, Theoretical; D056004:Molecular Dynamics Simulation