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.