MagiC

Software Package for Multiscale Coarse-Grained Modeling

MagiC is a software package designed to perform systematic coarse-graining of molecular models for multiscale simulations. MagiC takes input from atomistic trajectories computed by all-atom molecular dynamics program (such as GROMACS or MDynaMix), creates a coarse-grained trajectory according to a specified mapping scheme, computes radial distribution functions and distributions of bond lengths and angles between the coarse-grained sites, and finally uses iterative Boltzmann Inversion or Inverse Monte Carlo method to compute effective potentials for the coarse-grained model. Such potentials can be then further used for a large scale simulation.

The theory and basic principles behind MagiC are described in this paper:

A. Mirzoev, A.P.Lyubartsev "MagiC: Software Package for Multiscale Modeling" J. Chem. Theory and Computations, 9(3), 1512-1520 (2013) . DOI: 10.1021/ct301019v Abstract and Open Access Text

This is also the official reference.

Downloads:

Current stable version:

• MagiC-2.2 magic-2.2.1.tar.gz

  Documentation: User Guide 2.2: pdf

  On-line manual: User Guide 2.2: html

  Previous versions:

• MagiC-2.0.2 – magic-2.0.2.tar.gz

• MagiC-1.0.3.3 – magic-1.0.3.3.tar.gz (latest stable version of branch 1.0

Example-Tutorial:

• Solvent-mediated potentials between ions NaCl in water: Magic_Tutorial-NaCl.tar.gz

Developer version:

Get the most recent code from the repository using hg command (Mercurial should be installed):

hg clone https://bitbucket.org/magic-su/magic-2 -u magic-2.2

MagiC development page:

https://bitbucket.org/magic-su/magic-2

Here you can find the most recent updates, wiki-pages, supplementary information and even join the development process.

MagiC based publications:

Contact us:

Alexander Lyubartsev: alexander.lyubartsev@mmk.su.se Principal Investigator, Method development

Alexander Mirzoev, amirzoev@ntu.edu.sg Software development, Technical issues