EdgeExpansion

  • 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
  • See here for an example input file.

keywords

  • type: str, required
    • Evaluation type, "ee".
  • skip_frame: int, default=1
    • Number of frames to skip when ranking CVs.
    • 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)
    • Otherwise, you don't need to specify this option.

Papers

[1] Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins, https://doi.org/10.1063/5.0004654