RMSD

  • Evaluate snapshots of each trajectory so that the RMSD from the reference structure becomes larger.
  • The structure of the groups specified by selection1 and selection3 are superimposed by the least squares method and the RMSD is calculated with the structure of the groups specified by selection2 and selection4.
  • Usage Example
    • Sampling a wide range of structures
    • Sampling a wide range of ligand binding modes
  • See here for an example input file.

keywords

  • type: str, required
    • evaluation type, "rmsd"
  • threshold: float, required
    • PaCS-MD terminates the calculation when the evaluation value exceeds 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.
  • reference: str, required
    • Structure file path for the reference structure of RMSD calculation.
  • selection1: str, required
    • Selection string or name of index group for specified group in trajectories (least squares fit)
    • 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 (RMSD calculation)
    • 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)
  • 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.
    • This option is valid when analyzer="mdtraj" or analyzer="cpptraj".
    • If you use gromacs (analyzer="gromacs"), this option is ignored and the same selection indice are automatically used for your trajectories and the reference.
  • selection4: str, default=selection2
    • Selection string or name of index group for specified group in reference (RMSD 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.
    • This option is valid when analyzer="mdtraj" or analyzer="cpptraj".
    • If you use gromacs (analyzer="gromacs"), this option is ignored and the same selection indices are automatically used for your trajectories and the reference.

Papers

[1] Inhibition of the hexamerization of SARS-CoV-2 endoribonuclease and modeling of RNA structures bound to the hexamer, https://doi.org/10.1038/s41598-022-07792-2