A simplified force field for describing vibrational protein dynamics over the whole frequency range

Abstract : The empirical force fields used for protein simulations contain short-ranged terms (chemical bond structure, steric effects, van der Waals interactions) and long-ranged electrostatic contributions. It is well known that both components are important for determining the structure of a protein. We show that the dynamics around a stable equilibrium state can be described by a much simpler midrange force field made up of the chemical bond structure terms plus unspecific harmonic terms with a distance-dependent force constant. A normal mode analysis of such a model can reproduce the experimental density of states as well as a conventional molecular dynamics simulation using a standard force field with long-range electrostatic terms. This finding is consistent with a recent observation that effective Coulomb interactions are short ranged for systems with a sufficiently homogeneous charge distribution.
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https://hal.archives-ouvertes.fr/hal-02155539
Contributor : Laëtitia Legoupil <>
Submitted on : Thursday, June 13, 2019 - 4:30:13 PM
Last modification on : Tuesday, June 18, 2019 - 11:46:04 AM

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Konrad Hinsen, Gérald Kneller. A simplified force field for describing vibrational protein dynamics over the whole frequency range. Journal of Chemical Physics, American Institute of Physics, 1999, 111 (24), pp.10766-10769. ⟨10.1063/1.480441⟩. ⟨hal-02155539⟩

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