Schedule Jun 08, 2012
MagiC: A Software Package for Systematic Structure-based Coarse-graining
Alexander Mirzoev (Stockholm Univ.)

We introduce a software package which allows user to perform systematic structure-based coarse graining of molecular models using the Inverse Monte Carlo and Iterative Boltzmann Inversion methods. The effective pairwise potentials between coarse-grained (CG) sites (low resolution description) are constructed to reproduce structural distribution functions obtained from the reference system (high resolution description). The software supports CG tabulated intramolecular bond and angle interactions, as well as tabulated non-bonded interactions between different site types in the CG system, and treatment of long-range electrostatic forces by the Ewald summation. Two methods of effective potential refinement are implemented: Iterative Boltzmann Inversion having a simplified refinement scheme, which does not require much sampling; and inverse Monte Carlo method, which accounts for cross-correlations between pair interactions and thus has a faster convergence for a cost of extra sampling. MagiC uses its own Metropolis Monte Carlo sampling engine, which is efficiently parallelized providing fast convergence of the method and excellent scaling at parallel execution. The source code of MagiC is available in open access at

Author entry (protected)