MDAnalysis pipeline

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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Maintainers


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

Publication for MDAnalysis

MDAnalysis citations

 (3)
2018
PMCID: 5813003

[…] obtained simply by counting the number of permeation events per pore50., vmd51 was used for analysis and trajectory visualization, including rendering of trajectory snapshots. the gromacs tools and mdanalysis49 libraries were used in the analysis scripts., the free energy along the pore axis for ammonia was calculated using awh52,53. awh is an enhanced sampling algorithm which, within a single […]

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 […]

2014
PMCID: 4242812

[…] the stochastic component of the thermostat (bussi et al., 2007) would generate independent trajectories. in total, we simulated the dimer system for >10 µs., md trajectories were analyzed with mdanalysis (michaud-agrawal et al., 2011) and gromacs tools (hess, 2008). the distance d of the asp163–lys300 salt bridge was calculated as the minimum distance between the two carboxyl oδ1 and oδ2 […]

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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