Overview

MiMiCPy is a freely distributed component of the MiMiC package, consisting of tools to easily prepare and debug MiMiC input files, and to perform force matching to optimize MM parameters against QM/MM reference data. The instructions for installation are described in the MiMiCPy.

Commands for MiMiC input preparation

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

Commands for force matching

fm:

Run the force-matching workflow (DRESP + bonded optimization).

json2h5:

Convert large JSON force-matching datasets to HDF5.

h5info:

Inspect an HDF5 force-matching dataset (size, fields, counts).

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.

For more details about MiMiCPy, we refer to the following article:

B. Raghavan, F. K. Schackert, A. Levy, S. K. Johnson, E. Ippoliti, D. Mandelli, J. M. H. Olsen, U. Rothlisberger, and P. Carloni, MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations, J. Chem. Inf. Model. 63, 1406-1412 (2023). DOI: 10.1021/acs.jcim.2c01620