Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision | ||
|
eyes:logics:normalmodeanalysis [2017/06/12 17:52] jschlie1 |
eyes:logics:normalmodeanalysis [2017/06/12 18:32] jschlie1 |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| - | ====== Normal Mode Analysis ====== | + | ====== NormalModeAnalysis ====== |
| This logic performs a [[https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/images/1/17/Tirion1996_PRL.pdf| Normal Mode Analysis ]] (NMA) of the given 3D structure. It can be used to visualize basic molecular movement modes. | This logic performs a [[https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/images/1/17/Tirion1996_PRL.pdf| Normal Mode Analysis ]] (NMA) of the given 3D structure. It can be used to visualize basic molecular movement modes. | ||
| Line 45: | Line 45: | ||
| | Collectivity Score | Visualization of score vs. mode. The Collectivity Score is a metric that describes the amount of collective motion of pseudo atoms within one mode. It is normalized between 0 and 1. | | | Collectivity Score | Visualization of score vs. mode. The Collectivity Score is a metric that describes the amount of collective motion of pseudo atoms within one mode. It is normalized between 0 and 1. | | ||
| | Eigenvalues | Output of computed Eigenvalues. | | | Eigenvalues | Output of computed Eigenvalues. | | ||
| - | | Eigenvectors | Output of computed Eigenvectors.Pseudoatom visualization | This is a test output to allow the user to check the result of the fitting process. The number of pseudoatoms can be shown by double clicking the IO and clicking the 3D structure afterwards. | | + | | Eigenvectors | Output of computed Eigenvectors. | |
| ==== Apply Normal Modes ==== | ==== Apply Normal Modes ==== | ||
| Line 64: | Line 64: | ||
| ^ Output ^ Description ^ | ^ Output ^ Description ^ | ||
| | Intermediate states | Sequence of 3Ds that represent the position of the molecule at discrete time steps. | | | Intermediate states | Sequence of 3Ds that represent the position of the molecule at discrete time steps. | | ||
| - | |||
| - | ===== Additional Information ===== | ||
| - | |||
| - | |||
| - | |||
| - | |||
| - | |||