MD result analysis

Analyze Big DCD Fiels

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/

MDAnalysis(Python package)

http://pythonhosted.org/MDAnalysis/index.html

• 1. Overview over MDAnalysis
• 2. Selection Commands
• 3. Analysis modules
• 4. Topology modules
• 5. Coordinates modules
• 6. Selection exporters
• 7. Core modules
• 8. Visualization modules
• 9. MDAnalysis library
• 10. Version information for MDAnalysis — MDAnalysis.version
• 11. Constants and unit conversion — MDAnalysis.units
• 12. Custom exceptions and warnings — MDAnalysis.exceptions
• 13. References

Additional features available with MDanalysis

• fit a trajectory to a reference structure using the QCP RMSD-alignment code in MDAnalysis.core.qcprot (rmsfit_qcp.py);
• do a block-averaging error analysis (blocks.py);
• calculate a potential profile across a membrane (potential_profile.py);
• do a native contact analysis using MDAnalysis.analysis.contacts (nativecontacts.py)
• get the lipid composition of the individual leaflets of a bilayer using MDAnalysis.analysis.leaflet (membrane-leaflets.py);
• define the multimeric states of a number of transmembrane peptides via clustering (multimers-analysis.py);
• convert between trajectory formats (e.g. dcd2xtc.py or amber2dcd.py)
• use MDAnalysis for simple model building (make_MthK_tetramer.py);