MagiC: Software package for Multiscale Coarse-Grained Modelling.
User guide.
Version 2.2

Alexander Mirzoev$^{1,2,3}$ , Alexander Lyubartsev$^{3,4}$

Date: 3 May 2016

Abstract:

MagiC is a software package designed to perform systematic structure-based coarse graining of molecular models. The effective pairwise potentials between coarse-grained sites of low-resolution molecular models are constructed to reproduce structural distribution functions obtained from the modelling of the system in a high resolution (atomistic) description. The software contains tools to read atomistic trajectories generated by different simulation packages, create a coarse-grained trajectory, compute for it radial distribution functions as well as distributions of intramolecular bonds and angles, and then find effective potentials which reproduce these distributions in coarse-grained modeling. The software supports coarse-grained tabulated intramolecular bond and angle interactions, as well as tabulated non-bonded interactions between different site types in the coarse-grained system, with the treatment of long-range electrostatic forces by the Ewald summation. Two methods of effective potentials refinement are implemented: iterative Boltzmann inversion and inverse Monte Carlo, the later accounting for cross-correlations between pair interactions. MagiC uses its own Metropolis Monte Carlo sampling engine, which is efficiently parallelized providing fast convergence of the method and nearly linear scaling at parallel execution. The finally generated trajectories can be exported back to other software formats (e.g. GROMACS) for subsequent large scale simulations.