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

Major update v.3 is described in this paper:

A. Mirzoev, L. Nordenskiöld, A. P. Lyubartsev Magic v.3: An integrated software package for systematic structure-based coarse-graining Computer Physics Communications, 237, 263 - 273 (2019) DOI: 10.1016/j.cpc.2018.11.018

These papers are also the official references.

Downloads:

Current stable version:

MagiC-3.0 magic-3.0.tar.gz

Documentation: User Guide 3.0: pdf

On-line manual: User Guide 3.0: html
MagiC-2.2.1 – magic-2.2.1.tar.gz (last stable version of branch 2.0)
MagiC-1.0.3.3 – magic-1.0.3.3.tar.gz (last stable version of branch 1.0)

Example-Tutorials:

Solvent-mediated potentials between ions NaCl in water: Magic_Tutorial-NaCl.tar.gz
More tutorails available at: https://bitbucket.org/magic-su/magic_tutorials

Or can be downloaded by: git clone https://bitbucket.org/magic-su/magic_tutorials.git

Developer version:

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

git clone https://bitbucket.org/magic-su/magic-3.git

MagiC development page:

https://bitbucket.org/magic-su/magic-3

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

Contact us:

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

Alexander Mirzoev, amirzoev@gmail.com Software development, Technical issues