gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations

Irrgang, M. Eric; Hays, Jennifer M.; Kasson, Peter M.

doi:10.1093/bioinformatics/bty484

Cited by 10 publications

(4 citation statements)

References 6 publications

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“…We also benchmarked our calculations using Google Compute Engine in June 2018; the approximate cost of predicting a small molecule permeability was $1312 without extra discounts. Our approach permits further automation (without modifying the underlying method) for large-scale deployment using high-level simulation interfaces such as gmxapi [47] on either clusters or cloud-computing platforms. The goal of this would be twofold: large-scale deployment and elimination of any manual tuning for complete reproducibility.…”

Section: Discussionmentioning

confidence: 99%

Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics

Ferreira

Kasson

2019

ACS Infect. Dis.

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Crossing the gram-negative bacterial membrane poses a major barrier to antibiotic development, as many small molecules that can biochemically inhibit key bacterial processes are rendered microbiologically ineffective by their poor cellular uptake. The outer membrane is the major permeability barrier for many drug-like molecules, and the chemical properties that enable efficient uptake into mammalian cells fail to predict bacterial uptake. We have developed a computational method for accurate prospective prediction of outer-membrane uptake of drug-like molecules, which we combine with a new medium-throughput experimental assay. Parallel molecular dynamics simulations are used to successfully and quantitatively predict experimental permeabilities. For most polar molecules we test, outer membrane permeability also correlates well with whole-cell uptake. The ability to accurately predict and measure outer-membrane uptake of a wide variety of small molecules will enable simpler determination of which molecular scaffolds and which derivatives are most promising prior to extensive chemical synthesis. It will also assist in formulating a more systematic understanding of the chemical determinants of outer-membrane permeability.

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Section: Discussionmentioning

confidence: 99%

Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics

Ferreira

Kasson

2019

ACS Infect. Dis.

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“…We previously reported on gmxapi 0.0.4 [20], which allows Python driven molecular dynamics in GROMACS [21,22] to be extended at run time with custom researcher code.…”

Section: Introductionmentioning

confidence: 99%

gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support

2022

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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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“…We previously reported on gmxapi 0.0.4 13 , which allows Python driven molecular dynamics in GROMACS [14][15] to be extended at run time with custom researcher code. Here, we describe features present in gmxapi 0.2 and beyond, which offers both more advanced ensemble simulation logic and a feature-complete interface for GROMACS tools and analysis.…”

Section: Introductionmentioning

confidence: 99%

gmxapi: a GROMACS-native Python interface for molecular dynamics with ensemble and plugin support

Irrgang

Davis

Kasson

2021

Preprint

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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 installed by default in current versions of the software. Beyond simply wrapping GROMACS library operations, the API permits several advanced operations that are not feasible using the prior command-line interface. First, 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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gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 10 publications

References 6 publications

Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics

Antibiotic Uptake Across Gram-Negative Outer Membranes: Better Predictions Towards Better Antibiotics

gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support

gmxapi: a GROMACS-native Python interface for molecular dynamics with ensemble and plugin support

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