MDAnalysis Trajectory Analysis
Post-process molecular-dynamics trajectories into stability, flexibility, exposure, contact, and secondary-structure CSV outputs.
Overview
Analyze uploaded molecular-dynamics trajectories with MDAnalysis and MDTraj to calculate RMSD, RMSF, radius of gyration, hydrogen bonds, SASA, contacts, and DSSP secondary-structure summaries.
Run MDAnalysis Trajectory Analysis on Neurosnap
The MDAnalysis Trajectory Analysis online webserver allows anybody with a Neurosnap account to run and access MDAnalysis Trajectory Analysis, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong Terms of Use and Privacy Policy.
Features
- Analyzes uploaded trajectories without rerunning molecular dynamics.
- Calculates RMSD, RMSF, radius of gyration, SASA, hydrogen bonds, interface contacts, ligand-protein contacts, and DSSP.
- Uses CSV output names and column formatting consistent with OpenMM Molecular Dynamics and GROMACS Molecular Dynamics.
- Supports common trajectory formats including DCD, XTC, TRR, NetCDF, and multi-model PDB when paired with a compatible topology structure.
Statistics
Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.
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API Request
Access MDAnalysis Trajectory Analysis using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.
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Citations
Please cite the original work when using MDAnalysis Trajectory Analysis in publications or research outputs.
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Michaud-Agrawal, N. et al. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry, 2011. https://doi.org/10.1002/jcc.21787. |
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McGibbon, R. T. et al. MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophysical Journal, 2015. https://doi.org/10.1016/j.bpj.2015.08.015. |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |