What it does
The cosine content of the principal components is a good indicator for determining the quality of the sampling and can be used to determine the convergence of the MD simulation. This tool can calculate the cosine content of a user-defined PCA projection. Note: it uses zero-based indexes (i.e. 0 is the first principal component).
Input
- Trajectory file (DCD).
- PDB file.
Output
- The cosine content value.
- Tab-separated file of raw data of the first three principal components.