MagiC: Software package for Multiscale Coarse-Grained Modelling.
User guide.
Alexander Mirzoev
, Alexander Lyubartsev
Date: 31 October 2018
Abstract:
MagiC is a software package designed to perform systematic structure-based coarse-graining
of a wide range of molecular systems.. The effective pairwise potentials between coarse-grained sites of a low-resolution model 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 resulting CG-model can be exported to
high performance Molecular Dynamics software (such as LAMMPS, GROMACS, GALAMOST) for subsequent large-scale simulations.
