Extracting parameters for base-pair level models of DNA from molecular dynamics simulations |
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Authors: | Oscar Gonzalez John H Maddocks |
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Institution: | (1) Department of Mathematics, The University of Texas, Austin, TX 78712, USA, US;(2) Département de Mathématiques, école Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland, CH |
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Abstract: | A method is described to extract a complete set of sequence-dependent energy parameters for a rigid base-pair model of DNA
from molecular dynamics (MD) simulations. The method is properly consistent with equilibrium statistical mechanics and leads
to effective inertia parameters for the base-pair units as well as stacking and stiffness parameters for the base-pair junctions.
We give explicit formulas that yield a complete set of base-pair model parameters in terms of equilibrium averages that can
be estimated from a time series generated in an MD simulation. The expressions to be averaged depend strongly both on the
choice of coordinates used to describe rigid-body orientations and on the choice of strain measures at each junction.
Received: 12 July 2000 / Accepted: 5 January 2001 / Published online: 3 May 2001 |
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