Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian.

ABSTRACT: Coarse-graining of protein interactions provides a means of simulating large biological systems. Here, a coarse-graining method, REACH, is introduced, in which the force constants of a residue-scale elastic network model are calculated from the variance-covariance matrix obtained from atomistic molecular dynamics (MD) simulation. In test calculations, the C(alpha)-atoms variance-covariance matrices are calculated from the ensembles of 1-ns atomistic MD trajectories in monomeric and dimeric myoglobin, and used to derive coarse-grained force constants for the local and nonbonded interactions. Construction of analytical model functions of the distance-dependence of the interresidue force constants allows rapid calculation of the REACH normal modes. The model force constants from monomeric and

SUBMITTER: Moritsugu K 

PROVIDER: S-EPMC2072085 | biostudies-literature | 2007 Nov

REPOSITORIES: biostudies-literature