Dissociation

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

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

  • Usage Example

    • Ligand dissociating from a protein
    • Separate the distance between the two domains of a protein

  • See here for an example input file.

keywords

  • type: str, required
    • evaluation type, "dissociation".
  • threshold: float, required
    • PaCS-MD terminates the calculation when the evaluation value exceeds this threshold.
  • 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

[1] Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics, https://doi.org/10.1021/acs.jctc.7b00504
[2] Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model, https://doi.org/10.1021/acs.jpcb.8b10309
[3] Binding free energy of protein/ligand complexes calculated using dissociat
ion Parallel Cascade Selection Molecular Dynamics and Markov state model, http
s://doi.org/10.2142/biophysico.bppb-v18.037
[4] High pressure inhibits signaling protein binding to the flagellar motor an
d bacterial chemotaxis through enhanced hydration, https://doi.org/10.1038/s41
598-020-59172-3
[5] Dissociation Pathways of the p53 DNA Binding Domain from DNA and Critical
Roles of Key Residues Elucidated by dPaCS-MD/MSM, https://doi.org/10.1021/acs.
jcim.1c01508