ArticleJournal of chemical information and modeling2023
MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations.
Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- MiMiCPy-FM: A User-Friendly Force Matching Tool for Extending the Time Scale of QM/MM MD MiMiC Simulations.Journal of chemical information and modeling · 2026Article
- Multiphoton Absorption Spectra of Channelrhodopsin-2 via Multiscale Simulation Methods.Journal of chemical theory and computation · 2026Article
- Efficient, Hierarchical, and Object-Oriented Electronic Structure Interfaces for Direct Nonadiabatic Dynamics Simulations.Journal of chemical theory and computation · 2025Article
- Metal coordination and enzymatic reaction of the glioma-target R132H isocitrate dehydrogenase 1: Insights by molecular simulations.PloS one · 2025Article
- Transport mechanism of DgoT, a bacterial homolog of SLC17 organic anion transporters.The EMBO journal · 2024Article
- Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations.Journal of chemical information and modeling · 2023Review
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Authors and funding
9 authors.
Funding
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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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.