MDAnalysis specifications


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

MDAnalysis article

MDAnalysis citations

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 […]

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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