• max_cycle: int, default=1
  • Maximum number of cycles to run. (ex. 1, ..., 123, ..., 999)
• n_replica: int, default=1
  • Number of replica. (ex. 1, ..., 123, ..., 999)
• n_parallel: int, default=1
  • Number of replica calculated at a time
• centering: bool, default=True
  • Whether to bring the molecule selected by centering_selection to the center of the simulation cell when creating the initial structure for the next cycle
• centering_selection: str, default="protein" or "Protein" or "@CA,C,O,N,H"
  • Molecules to be moved to the center
  • default value will be changed to match analyzer
    • if analyzer == "mdtraj", default="protein"
    • if analyzer == "gromacs", default="Protein"
    • if analyzer == "cpptraj", default="@CA,C,O,N,H"
• working_dir: str, default="./."
  • Directory where pacsmd will run
• rmmol: bool, default=false
  • Whether rmmol is executed after each cycle
• keep_selection: str, (required if rmmol=true)
  • Molecular name or index group to be left in the trajectory when rmmol
• rmfile: bool, default=false
  • Whether rmfile is executed after trial

• simulator: str, required
  • Software used inside PaCS-MD
• cmd_mpi: str, default=""
  • Commands for MPI such as mpirun, blank is OK
• cmd_serial: str, required
  • Commands to run the simulator serially
• cmd_parallel: str, default=cmd_serial
  • Commands to run the simulator parallelly
• structure: str, required
  • Structural file such as gro, pdb, rst7, etc.
• topology: str, required
  • Topology file such as top, parm7, psf, etc.
• mdconf: str, required
  • Parameter file such as mdp, mdin, namd, etc.
• index_file: str, (required if Gromacs)
  • Gromacs index file
• trajectory_extension: str, required
  • Trajectory file extension. ("." is necessary)
• nojump: bool, default=false
  • whether to execute -pbc nojump treatment for the selection feature calculation in analayzer, snapshot extraction in exporter and performing rmmol
  • valid only when analyzer is also gromacs
  • If true, molecules are allowed to get out of the simulation box in order to avoid the error in MSM due to the jumping of break of the molecule over pbc box.
  • If false, molecules are just made whole by -pbc mol and can warp across the pbc box.
  • Be noted that the output prd.xtc files are not processed with these -pbc options. (only prd_rmmol.xtc files are processed)
  • This option is recommended to use when a/dissociation and a_d pacsmd is performed using gromacs as simulator and analyzer
  • nojump=true can lead too large coordinate value to cause overflow or loss-of-significane problem. It will not happpen in most cases, but be carefull if your ligand is very small and simulation box is very large.
  • When this options is applied, analyzer can consider the distance even if ligand exceeds simulation box
  • This option is not present in example input in the sample input repository since this option was added in version 1.1.0

• simulator: str, required
  • Software used inside PaCS-MD
• cmd_mpi: str, default=""
  • Commands for MPI such as mpirun, blank is OK
• cmd_serial: str, required
  • Commands to run the simulator serially
• cmd_parallel: str, default=cmd_serial
  • Commands to run the simulator parallelly
• structure: str, required
  • Structural file such as gro, pdb, rst7, etc.
• topology: str, required
  • Topology file such as top, parm7, psf, etc.
• mdconf: str, required
  • Parameter file such as mdp, mdin, namd, etc.
• trajectory_extension: str, required
  • Trajectory file extension. ("." is necessary)

• simulator: str, required
  • Software used inside PaCS-MD
• cmd_mpi: str, default=""
  • Commands for MPI such as mpirun, blank is OK
• cmd_serial: str, required
  • Commands to run the simulator serially
• cmd_parallel: str, default=cmd_serial
  • Commands to run the simulator parallelly
• structure: str, required
  • Structural file such as gro, pdb, rst7, etc.
• topology: str, required
  • Topology file such as top, parm7, psf, etc.
• mdconf: str, required
  • Parameter file such as mdp, mdin, namd, etc.
• trajectory_extension: str, required
  • Trajectory file extension. ("." is necessary)

• type: str, required
  • evaluation type, "target".
• 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.
• 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 indices 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.

• 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 indices 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.

• 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)

• 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)

• 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.

• type: str, required
  • evaluation type, "a_d".
• 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 is only supported)
• 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 is only supported)
• d_threshold: float, required
  • Threshold for switching from dissociation to association mode. If the maximum value of cv calculated while in dissociation mode exceeds this value, it switches to associtaion mode.
• frame_sel: int, required
  • One of the conditions used to switch from association to dissociation.
  • If the highest ranking frame in association mode is less than this value, it is judged that there has been no change from the previous cycle (i.e., it has come as close as it can).　Also, at this time, we consider it to be within bound.
• bound_threshold: int, required
  • One of the conditions used to switch from association to dissociation.
  • When the number of bound cycles exceeds this value, the mode is switched from association to disassociation and the number of bound cycles is initialized to 0. When the number of bound cycles exceeds this value, the mode is switched from association to disassociation and the number of bound cycles is initialized to 0.

• type: str, required
  • Evaluation type
• skip_frame: int, default=1
  • Number of frames to skip when ranking CVs
• threshold: float, required
  • CV threshold for determining to terminate a trial

Template type is a type that can be defined by the user. It is possible to include user-specific variables in input.toml, and these variables can be used in template type in which they are defined. For more information, click here.

• cmd_gmx: str
  • Gromacs command (ex. gmx, gmx_mpi)
  • will be created from cmd_serial
• top_mdtraj: str
  • topology file for mdtraj
  • will be created from input.toml
• structure_extension: str
  • Structure file extension
  • will be created from structure