Sökning: id:"swepub:oai:DiVA.org:uu-365010" >
gmxapi :
gmxapi : a high-level interface for advanced control and extension of molecular dynamics simulations.
-
- Irrgang, M Eric (författare)
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
-
- Hays, Jennifer M (författare)
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
-
- Kasson, Peter M. (författare)
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
-
Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA. (creator_code:org_t)
- 2018-06-15
- 2018
- Engelska.
-
Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 34:22, s. 3945-3947
- Relaterad länk:
-
https://uu.diva-port... (primary) (Raw object)
-
visa fler...
-
https://academic.oup...
-
https://urn.kb.se/re...
-
https://doi.org/10.1...
-
visa färre...
Abstract
Ämnesord
Stäng
- Summary: Molecular dynamics simulations have found use in a wide variety of biomolecular applications, from protein folding kinetics to computational drug design to refinement of molecular structures. Two areas where users and developers frequently need to extend the built-in capabilities of most software packages are implementing custom interactions, for instance biases derived from experimental data, and running ensembles of simulations. We present a Python high-level interface for the popular simulation package GROMACS that 1) allows custom potential functions without modifying the simulation package code, 2) maintains the optimized performance of GROMACS, and 3) presents an abstract interface to building and executing computational graphs that allows transparent low-level optimization of data flow and task placement. Minimal dependencies make this integrated API for the GROMACS simulation engine simple, portable, and maintainable. We demonstrate this API for experimentally-driven refinement of protein conformational ensembles.Availability: LGPLv2.1 source and instructions are available at https://github.com/kassonlab/gmxapi.Supplementary information: Supplementary data are available at Bioinformatics online.
Ämnesord
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Datavetenskap (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Computer Sciences (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Programvaruteknik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Software Engineering (hsv//eng)
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
Hitta via bibliotek
Till lärosätets databas