Association

• Evaluate snapshots of each trajectory so that the centers of mass of the two selected groups are close together.

• The two selected groups are selection1 and selection2 in the input file.

• Usage Example

  • Bringing a ligand closer to a protein
  • Bringing two domains of a protein closer together

• See here for an example input file.

keywords

• type: str, required
  • evaluation type, "association".
• threshold: float, required
  • PaCS-MD terminates the calculation when the evaluation value falls below this threshold (in units of nm).
• 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.
  • "mdtraj", "gromacs" and "cpptraj" are supported.
• selection1: str, required
  • Selection string or name of index group for specified group in trajectories
  • Depending on the analyzer, there are different ways to specify selection.
    • If you use mdtraj (analyzer="mdtraj"), the selection should follow mdtraj's atom selection. e.g. "resid 5 to 100 and name CA"
    • If you use gromacs (analyzer="gromacs"), the selection should follow Gromacs index group in index.ndx. (Gromacs supported only)
• selection2: str, required
  • Selection string or name of index group for specified group in trajectories
  • Depending on the analyzer, there are different ways to specify selection.
    • If you use mdtraj (analyzer="mdtraj"), the selection should follow mdtraj's atom selection. e.g. "resid 5 to 100 and name CA"
    • If you use gromacs (analyzer="gromacs"), the selection should follow Gromacs index group in index.ndx. (Gromacs supported only)

Papers