Paper Citing NAMD - Abstract
Sinitskiy, Anton V.; Voth, Gregory A.
Coarse-graining of proteins based on elastic network models
CHEMICAL PHYSICS, 422:165-174, AUG 30 2013
To simulate molecular processes on biologically relevant length-and timescales, coarse-grained (CG) models of biomolecular systems with tens to even hundreds of residues per CG site are required. One possible way to build such models is explored in this article: an elastic network model (ENM) is employed to define the CG variables. Free energy surfaces are approximated by Taylor series, with the coefficients found by force-matching. CG potentials are shown to undergo renormalization due to roughness of the energy landscape and smoothing of it under coarse-graining. In the case study of hen egg-white lysozyme, the entropy factor is shown to be of critical importance for maintaining the native structure, and a relationship between the proposed ENM-mode-based CG models and traditional CG-bead-based models is discussed. The proposed approach uncovers the renormalizable character of CG models and offers new opportunities for automated and computationally efficient studies of complex free energy surfaces. (C) 2013 Elsevier B. V. All rights reserved.
