Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Mar 13;63(5):1406-1412.
doi: 10.1021/acs.jcim.2c01620. Epub 2023 Feb 22.

MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations

Bharath Raghavan  1   2 , Florian K Schackert  1   2 , Andrea Levy  3 , Sophia K Johnson  3 , Emiliano Ippoliti  1 , Davide Mandelli  1 , Jógvan Magnus Haugaard Olsen  4 , Ursula Rothlisberger  3 , Paolo Carloni  1   2
Affiliations

MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations

Bharath Raghavan et al. J Chem Inf Model. .

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.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing financial interest.

Figures

Figure 1
Figure 1
Flowchart of the generation of the CPMD and GROMACS input files for a MiMiC-based QM/MM simulation.
Figure 2
Figure 2
Organization of the main classes in MiMiCPy.
See this image and copyright information in PMC

References

    1. Merz K. M. Using quantum mechanical approaches to study biological systems. Acc. Chem. Res. 2014, 47, 2804–2811. 10.1021/ar5001023. - DOI - PMC - PubMed
    1. Brookes J. C. Quantum effects in biology: golden rule in enzymes, olfaction, photosynthesis and magnetodetection. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 2017, 473, 20160822.10.1098/rspa.2016.0822. - DOI - PMC - PubMed
    1. Cole D. J.; Hine N. D. Applications of large-scale density functional theory in biology. J. Phys.: Condens. Matter 2016, 28, 393001.10.1088/0953-8984/28/39/393001. - DOI - PubMed
    1. Van Der Kamp M. W.; Mulholland A. J. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry 2013, 52, 2708–2728. 10.1021/bi400215w. - DOI - PubMed
    1. Liu M.; Wang Y.; Chen Y.; Field M. J.; Gao J. QM/MM through the 1990s: The First Twenty Years of Method Development and Applications. Isr. J. Chem. 2014, 54, 1250–1263. 10.1002/ijch.201400036. - DOI - PMC - PubMed

Publication types