Abstract
MiMiC is a highly flexible, extremely scalable multiscale modeling framework. It couples the CPMD (quantum mechanics, QM) and GROMACS (molecular mechanics, MM) codes. The code requires preparing separate input files for the two programs with a selection of the QM region. This can be a tedious procedure prone to human error, especially when dealing with large QM regions. Here, we present MiMiCPy, a user-friendly tool that automatizes the preparation of MiMiC input files. It is written in Python 3 with an object-oriented approach. The main subcommand PrepQM can be used to generate MiMiC inputs directly from the command line or through a PyMOL/VMD plugin for visually selecting the QM region. Many other subcommands are also provided for debugging and fixing MiMiC input files. MiMiCPy is designed with a modular structure that allows seamless extensions to new program formats depending on the requirements of MiMiC.
| Original language | English |
|---|---|
| Pages (from-to) | 1406-1412 |
| Number of pages | 7 |
| Journal | Journal of Chemical Information and Modeling |
| Volume | 63 |
| Issue number | 5 |
| DOIs | |
| State | Published - Mar 13 2023 |
| Externally published | Yes |
Funding
We thank CECAM for providing an opportunity to present the code at the flagship school in July 2022. We thank Viacheslav Bolnykh and Mathilde Goullieux for valuable suggestions. B.R., D.M., and P.C. thank the Helmholtz European Partnering program (“Innovative high-performance computing approaches for molecular neuromedicine”) for funding. J.M.H.O. thanks VILLUM FONDEN for funding (grant no. 29478), and U.R. acknowledges funding from the Swiss National Science Foundation Grant No. 200020-185092.