MDAnalysis specifications

Information

Unique identifier	OMICS_18200
Name	MDAnalysis
Software type	Package/Module
Interface	Command line interface
Restrictions to use	None
Operating system	Mac OS
Programming languages	C, Python
License	GNU General Public License version 2.0
Computer skills	Advanced
Version	0.16.0
Stability	Stable
Requirements	Numpy
Maintained	Yes

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Documentation

Documentation: http://www.mdanalysis.org/mdanalysis/

Maintainers

Oliver Beckstein <>
Naveen Michaud-Agrawal <>
Elizabeth Denning <>
Thomas Woolf <>

MDAnalysis article

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

2011 J Comput Chem

PMID: 21500218

DOI: 10.1002/jcc.21787

MDAnalysis citations

(2)

Assembling the Tat protein translocase

2016

PMCID: 5201420

[…] of non-bonded contacts,using lennard-jones parameters. simulations were performed with an integration timestep of 2 fs., md simulations were analyzed using gromacs tools (hess et al., 2008), mdanalysis (michaud-agrawal et al., 2011), and locally written code. all images and animations were generated using pymol (delano, 2002)., strains used in this work are listed in table 2. for aq8a […]

Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance

2015

PMCID: 4681344

[…] as implemented in ambertools14 (53). interaction energies between waters referred to as w1-4 in the text and the binding pocket residues of pb1(5) and brd4(1) were analyzed using the python toolkit mdanalysis (54) and the gromacs tools. four spherical hydration sites with 1.2-å radius were defined and centered on the crystallographic water coordinates; for pb1(5), the water positions were taken […]

MDAnalysis institution(s)

Department of Biophysics and of Physiology, Johns Hopkins School of Medicine, Baltimore, MD, USA; Department of Pharmaceutical Chemistry, University of Maryland, Baltimore, School of Pharmacy, Baltimore, MD, USA; Department of Biochemistry, University of Oxford, Oxford, UK

MDAnalysis funding source(s)

Supported in part by a grant from the National Institutes of Health (GM064746), the European Union (EDICT Project, grant 201924) and in part by a Junior Research Fellowship at Merton College, Oxford.

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