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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 |
Download
Versioning
No version available
Documentation
- Documentation: http://www.mdanalysis.org/mdanalysis/
Maintainers
- person_outline Oliver Beckstein
- person_outline Naveen Michaud-Agrawal
- person_outline Elizabeth Denning
- person_outline Thomas Woolf
Publication for MDAnalysis
MDAnalysis citations
(65)Clinically relevant mutations in the ABCG2 transporter uncovered by genetic analysis linked to erythrocyte membrane protein expression
[…] nd mutant NBDs using GROMACS with CHARMM36m force field,. For simulation details see the Supplementary materials. Analysis was performed by employing GROMACS tools, VMD Network Wizard Plugin, and the MDAnalysis Python package. […]
Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations
[…] Unless stated otherwise, analyses of MD trajectories are performed using Python 2.7 and the MDAnalysis module (version 0.15.0) []. Matplotlib is used for plotting data []. VMD is used for visualization of trajectories and production of structural figures [–]. For each substrate state, a sing […]
Crystal structure of undecaprenyl pyrophosphate phosphatase and its role in peptidoglycan biosynthesis
[…] parameters, with a Verlet cutoff scheme to permit GPU calculation of non-bonded contacts. Simulations were performed with an integration time step of 2 fs. The MDS were analyzed using Gromacs tools, MDAnalysis and locally written python and perl scripts.Homologous sequences were identified in the UniProtKB database, using eight iterations of Jackhmmer, with the default search parameters. This ide […]
Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function
[…] idues. For the permeability calculation we for practical purposes used the center of geometry instead of the COM.Pore radii were calculated using HOLE v.2.2.004.Hydrogen bonds were detected using the MDAnalysis hydrogen bond library, applying a donor-acceptor atom distance cutoff 3.5 Å and a donor-hydrogen-acceptor cutoff angle of 150° (where 180° is linear).The osmotic permeability, pf was calcul […]
Balancing Force Field Protein–Lipid Interactions To Capture Transmembrane Helix–Helix Association
[…] Visualization was done using VMD, and analysis was done using MDAnalysis. […]
Solvation dynamics in polar solvents and imidazolium ionic liquids: failure of linear response approximations† †Electronic supplementary information (ESI) available: Higher order and partial correlation functions, corrections to Gaussian statistics and structure analysis for all systems. See DOI: 10.1039/c7cp07052g
[…] of starting configurations. To the best of our knowledge, no simulation study of the Stokes shift exists on such a large scale. The resulting trajectories were analyzed via a python program based on MDAnalysis. 95% confidence intervals are given, where appropriate, as where x is the average of the property of interest, t the Student t factor, s the standard deviation and n the number of independ […]
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