ArticlePLoS computational biology2022
gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
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- Machine Learning and Molecular Modeling Strategy for the Identification of CNS-Active Acetylcholinesterase Inhibitors.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Exploratory identification of lycorine as a potential inhibitor of the ACP2/YME1L1 prognostic axis in esophageal squamous cell carcinoma: a multi-omics and computational hypothesis.Molecular genetics and genomics : MGG · 2026Article
- Deciphering the Effect of Methyl 4‑Hydroxybenzoate on Breast Cancer by Bioinformatics and Experiments.ACS omega · 2026Article
- ST-Analyzer: A Packaged Web and Command-Line Interface for Simulation Trajectory Analysis.bioRxiv : the preprint server for biology · 2026Article
- 3D-QSAR, Molecular Docking, Molecular Dynamics Simulation, and Pharmacokinetic Prediction of 1H-Pyrazolo[3,4-d]pyrimidine Derivatives as PI3Kδ Inhibitors.Current medicinal chemistry · 2026Article
- Integrated Molecular Docking and Dynamic Simulations Reveal Glycyrrhizic Acid Alleviates Allergic Rhinitis in Rats by Inhibiting the TLR4/NF-κB/IL-1β Pathway.Journal of immunology research · 2026Article
- Identification of potential COVID-19 Mpro inhibitors through covalent drug docking, molecular dynamics simulation, and MMGBSA calculation.Scientific reports · 2025Article
- ProGuide: a flexible framework for modeling global conformational rearrangements in proteins using DEER-derived distance restraints.bioRxiv : the preprint server for biology · 2025Article
- Potential Mechanisms of Tetramethylpyrazine in the Treatment of Traumatic Brain Injury Based on Network Pharmacology, Molecular Docking, Molecular Dynamics Simulations, and in vivo Experiments.International journal of general medicine · 2025Article
- Article
- The Effect of Acidic Residues on the Binding between Opicalcin1 and Ryanodine Receptor from the Structure-Functional Analysis.Journal of natural products · 2024Article
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Authors and funding
3 authors.
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Abstract
Gmxapi provides an integrated, native Python API for both standard and advanced molecular dynamics simulations in GROMACS. The Python interface permits multiple levels of integration with the core GROMACS libraries, and legacy support is provided via an interface that mimics the command-line syntax, so that all GROMACS commands are fully available. Gmxapi has been officially supported since the GROMACS 2019 release and is enabled by default in current versions of the software. Here we describe gmxapi 0.3 and later. Beyond simply wrapping GROMACS library operations, the API permits several advanced operations that are not feasible using the prior command-line interface. First, the API allows custom user plugin code within the molecular dynamics force calculations, so users can execute custom algorithms without modifying the GROMACS source. Second, the Python interface allows tasks to be dynamically defined, so high-level algorithms for molecular dynamics simulation and analysis can be coordinated with loop and conditional operations. Gmxapi makes GROMACS more accessible to custom Python scripting while also providing support for high-level data-flow simulation algorithms that were previously feasible only in external packages.
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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.