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Difference between revisions from 2010/11/22 14:01 and 2009/10/21 10:00.
Cuby comes with a set of scripts helping to prepare calculations and work with the results.

!Submitting cuby job to queue system

!Geometry format conversion
*[geometry2xyz] - Format conversion: to .xyz
*[geometry2pdb] - Format conversion: to PDB file

!Geometry manipulation
*[geometry] - basic operations with geometry
*[geometry_pdbtools] - operations specific to PDB files
*[geometry_fragmentation] - script handling multiple tasks useful when preparing fragmented calculation.
*[geometry_scan] - generate series of geometries by varying internal coordinates

!Analysis of the results
*[et_paths] - search for the most probable electron transfer paths in trajectory from MD
*[measure] - geometric measurements in MD trajectory


!Other tools
*[optimize_parameters] - universal optimizer of externally provided function