Freeform Conf Energies

This cube estimates the Gibbs free energy to convert an ensemble

of solution conformations into a state where only a single specific conformation is present.

The calculated energies are added to the intake port record and emitted through the success port.

Related Cubes

Calculation Parameters

  • 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
  • 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
  • Force field (string) : Force field model to be used. Built-in types are: MMFF94S, Smirnoff99Frost, PARSLEY_OPENFF100, PARSLEY_OPENFF111, PARSLEY_OPENFF120. The name of a .offxml file that defines a SMIRNOFF force field can also be used as input.
    Default: MMFF94S
  • GPUs (integer) : The number of GPUs to run this cube with
    Default: 0 Max: 16
  • Include input conformer (boolean) : Flag to include the input conformers in ensemble
    Default: False
  • 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
  • Max Rotors (integer) : Cutoff of rotatable bonds. The cube will skip molecules with rotors more than the cutoff.
    Default: 20 Min: 1 Max: 9999
  • 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 All Results (boolean) : Output all available single conformer results. If set to False, only the more important results are reported
    Default: True
  • Spot policy (string) : Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Use input ensemble (boolean) : Flag to use input ensemble conformers
    Default: False

Field parameters

  • Delta G field (Field Type: Float) : Free energy of selecting the conformer from the ensemble
    Default: Delta G
  • Total entropy field (Field Type: Float) : Total entropy of the conformer ensemble
    Default: Total entropy
  • None (Field Type: StringVec) : Message extended log field
    Default: Extended Log Field
  • None (Field Type: Chem.Mol) :
  • Intra-molecular energy field (Field Type: Float) : Total intermolecular energy of the conformer
    Default: Intra-molecular energy
  • ln Qrot field (Field Type: Float) : Natural logarithm of the conformer rotational partition function
    Default: ln Qrot
  • ln Qvib field (Field Type: Float) : Natural logarithm of the conformer vibrational partition function
    Default: ln Qvib
  • None (Field Type: String) : Message log field
    Default: Log Field
  • None (Field Type: Chem.Mol) :
  • Probability of state field (Field Type: Float) : Probability of state associated with the conformer
    Default: Probability of state
  • Relative energy field (Field Type: Float) : Relative energy of the conformer with respect to the lowest energy conformer of the ensemble
    Default: Relative energy
  • Relative lnQ field (Field Type: Float) : Natural logarithm of the relative vibrational-rotational partition function with respect to the lowest free energy conformer in the ensemble
    Default: Relative lnQ
  • Rotational Entropy field (Field Type: Float) : Rotational entropy of the conformer
    Default: Rotational Entropy
  • Solvation energy field (Field Type: Float) : Solvation energy of the conformer
    Default: Solvation energy
  • Total energy field (Field Type: Float) : Total (intramolecular + solvation) energy of the conformer
    Default: Total energy
  • Vibrational Entropy field (Field Type: Float) : Vibrational entropy of the conformer
    Default: Vibrational Entropy

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 Freeform Conf Energies

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: snowball/freeform/freeform_conf_dG.py