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1) A rigid-body MD program to simulate coarse-grained RNA. 2) Derive RNA parameters at the functional group level. 3) A program to interconvert between coarse-grained and all-atom structure. Visualization by PDB viewer and SimTk ToRNADo.

This project aims to develop a coarse-grained (CG) model for RNA at the functional group, residue as well as secondary structure level. In the functional group-based model, each sugar ring, phosphate backbone and base group will be represented as a CG particle. The “shape” of the particle is described by the anisotropic Gay-Berne function. Point multipoles are placed at the center and selected off-center sites. This model has been shown successful in describing hydrogen-bonded molecular liquids (see publication).