Absolute versus relative entropy parameter estimation in a coarse-grain model of DNA

A description of a method based on maximum absolute entropy principle for fitting an observed matrix of covariances for the cgDNA coarse grain model. In this fitting procedure we also allow indefinite local stiffness-matrix parameter blocks, that nevertheless always generate a positive-definite model stiffness matrix. Due to the intrinsic linear structure of DNA and the convergence characteristics of the MD time series data, the maximum absolute entropy parameter set yields significantly improved predictions of persistence lengths, when compared to a previous parameter set that was fit to the same MD data, but using a maximum relative entropy fitting principle and local stiffness-matrix parameter blocks that were constrained to be semi-definite.

The cgDNAparamset2 described in the article is available for download.