Psi4 Conformer Generation

Dense conformer generation Cube for QM calculations

Related Cubes

Calculation Parameters

  • Conformer Index Prefix (string) : Prefix for conformer index number.
    Default: Conformer_
  • CPUs (integer) : The number of CPUs to run this cube with
    Default: 1 Min: 1 Max: 128
  • Cube Metrics (string) : Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Custom Torsions (boolean) : Flag indicating if user-defined custom torsion library is to be used
    Default: False
  • Custom Torsion Library (string) : Torsion sampling rules separated by $$$
    Default: “”
  • Temporary Disk Space (MiB) (decimal) : The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 Min: 128.0 Max: 8589934592
  • Energy Window (decimal) : Energy window for conformer selection
    Default: 100.0 Max: 10000000000.0
  • GPUs (integer) : The number of GPUs to run this cube with
    Default: 0 Max: 16
  • Instance Tags (string) : Only run on machines with matching tags (comma separated)
    Default: “”
  • Instance Type (string) : The type of instance that this cube needs to be run on
  • Maximum number of fragment model conformers to keep (integer) : Maximum number of fragment conformations to keep
    Default: 100 Min: 1 Max: 1000
  • Maximum fragment RMSD (decimal) : Maximum RMSD for fragment model deduplication
    Default: 0.1 Max: 1.0
  • Memory (MiB) (decimal) : The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 Min: 256.0 Max: 8589934592
  • Metric Period (decimal) : How often to sample metrics, in seconds
    Default: 60 Min: 1 Max: 300
  • Output intermediate fragment conformers (boolean) :
    Default: False
  • Output parent molecule for remerging conformers (boolean) : By default (False) conformers are output as their own records. If you would like to merge the conformers back together, set this parameter to True.
    Default: False
  • RMSD Threshold (decimal) : RMSD threshold for conformer duplicate removal
    Default: 0.5 Max: 5.0
  • Rotor Offset Compression (boolean) : Flag indicating if rotor offset compression be turned on. With rotor offset compression turned on, the atoms in the molecule are also reordered and the generated conformers are more deterministic.
    Default: False
  • Sample Hydrogens (boolean) : Sets whether hydrogens will be sampled. This option will enable sampling of hydrogen locations for -OH, -SH, and amines.
    Default: True
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Strict Stereo (boolean) : Flag indicating if all chiral atoms and bonds must have specified stereo
    Default: True

Field parameters

  • Conformer Index Field Name (Field Type: String) : Conformer index field name.
    Default: Conformer_Index
  • Energy Field (Field Type: Float) : Energy Field
    Default: FF Energy
  • Extended Log Field (Field Type: StringVec) : Message extended log field
    Default: Extended Log Field
  • Input Molecule Field (Field Type: Chem.Mol) : Primary Molecule Field to use as input to the Cube
  • Log Field (Field Type: String) : Message log field
    Default: Log Field
  • Output Molecule Field (Field Type: Chem.Mol) : Primary Molecule Field to use as output to the Cube

Hardware Parameters

Machine hardware requirements

  • Memory (MiB) (decimal) : The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 Min: 256.0 Max: 8589934592
  • Temporary Disk Space (MiB) (decimal) : The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 Min: 128.0 Max: 8589934592
  • GPUs (integer) : The number of GPUs to run this cube with
    Default: 0 Max: 16
  • CPUs (integer) : The number of CPUs to run this cube with
    Default: 1 Min: 1 Max: 128
  • Instance Type (string) : The type of instance that this cube needs to be run on
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (string) : Only run on machines with matching tags (comma separated)
    Default: “”

Metrics Parameters

Cube Metric Parameters

  • Metric Period (decimal) : How often to sample metrics, in seconds
    Default: 60 Min: 1 Max: 300
  • Cube Metrics (string) : Set of metrics to be collected

    Choices: cpu, disk, memory, network

Parallel Psi4 Conformer Generation

The parallel version adds these extra parameters.

  • Number of messages to distribute at a time (integer) : The maximum number of messages to bundle together for a parallel cube.
    Default: 1 Min: 1 Max: 65535
  • Maximum Failures (integer) : The maximum number of times to attempt processing a work item
    Default: 10 Min: 1 Max: 100
  • Autoscale this Cube (boolean) : If True, let Orion manage the parallelism of this Cube
    Default: True
  • Maximum number of Cubes (integer) : The maximum number of concurrently running copies of this Cube
    Default: 1000 Min: 1
  • Minimum number of Cubes (integer) : The minimum number of concurrently running copies of this Cube
    Default: 0

Tip

filename: psi4-orion/psi4_orion/psi4_cube_conf.py