Evaluate snapshots of each trajectory so that the frame forms the convex hull of the 4-dimentional principal component space(PCs).
Snapshots of each cycle are projected onto a 4-dimensional principal component spaces (PCs). Its convex hull is computed and the initial structure of the next cycle is selected from the polygon's vertices.
Usage Example
Sampling a wide range of phase space without knowing the reference structure
If you set skip_frame=2, PaCS-MD will use every other frame.
analyzer: str, default="mdtraj"
Trajectory tool used to calculate the evaluation value.
only "mdtraj" is supported.
reference: str, required
Trajectory file used to compute the covariance matrix in Principal Component Analysis (PCA).
If this value is not set, the covariance matrix is computed based on the trajectory of cycle 0.
selection1: str, required
Selection string or name of index group for specified group in trajectories (least squares fit)
If you use mdtraj (analyzer="mdtraj"), the selection should follow mdtraj's atom selection.
selection2: str, required
Selection string or name of index group for specified group in trajectories (PCA calculation)
No correction by atomic weights or number of atoms is made when calculating the covariance matrix or projecting.
If you use mdtraj (analyzer="mdtraj"), the selection should follow mdtraj's atom selection.
selection3: str, default=selection1
Selection string or name of index group for specified group in reference (least squares fit)
If your reference structure has different topology from your trajectories, you can utilize this option. (e.g. reference has different configuration about mutation, missing residues or modified residues from your the trajectories)
Otherwise, you don't need to specify this option.
selection4: str, default=selection2
Selection string or name of index group for specified group in reference (PCA calculation)
If your reference structure has different topology from your trajectories, you can utilize this option. (e.g. reference has different configuration about mutation, missing residues or modified residues from your the trajectories)