Overview

MiMiCPy is a freely distributed component of the MiMiC package, consisting of tools to easily prepare and debug MiMiC input files. The instructions for installation are described in the MiMiCPy.

MiMiCPy primarily consists of a set of command line tools to easily prepare and debug complex CPMD and GROMACS input files for a MiMiC run. The list of tools are:

PrepQM: Prepare the QM and MM input files from MM data
CPMD2Coords: Convert the atom coordinates in a CPMD/MiMiC input file to a GRO or PDB file
FixTop: Fix the [ atomtypes ] section of the GROMACS MM topology for a MiMiC run
CPMDid: Find the CPMD indices of QM and MM atoms in the system
Geom2Coords: Convert the atom coordinates in a CPMD GEOMETRY file to a GRO or PDB file

Each tool is described in following sections. In addition to the command line tools, plugins of the PrepQM tool for VMD and PyMOL have also been provided. MiMiCPy can also be used as a Python library for more advanced functionalities.

License

MiMiCPy is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

MiMiCPy is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this program. If not, see http://www.gnu.org/licenses/.