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 (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Cube Metrics (cube_metrics) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network
  • Temporary Disk Space (MiB) (disk_space) type: 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 (ff_type) type: string: Built-in force field model to be used.
    Default: sage
    Choices: mmff94s, parsley, sage
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Include input conformer (include_input) type: boolean: Flag to include the input conformers in ensemble. Setting this to true would add the input conformers to the internally generated conformers.
    Default: False
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Ionic state (ionic_state) type: string: Ionic state of molecules to be used
    Default: ph74
    Choices: ph74, uncharged, input
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • Max Rotors (max_rotors) type: integer: Cutoff of rotatable bonds. The cube will skip molecules with rotors more than the cutoff.
    Default: 40 , Min: 1, Max: 9999
  • Memory (MiB) (memory_mb) type: 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 (metric_period) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Output All Results (output_all_res) type: boolean: Output all available single conformer results. If set to False, only the more important results are reported
    Default: True
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Use input ensemble (use_inp_ens) type: boolean: Flag to use input ensemble conformers. Setting this to true would bypass any new conformer generation.
    Default: False

Field parameters

  • Delta G field (delta_g_field) type: Field Type: Float: Free energy of selecting the conformer from the ensemble
    Default: Delta G
  • Total entropy field (ens_ent_field) type: Field Type: Float: Total entropy of the conformer ensemble
    Default: Total entropy
  • Extended Log Field (ext_log_field) type: Field Type: StringVec: Message extended log field
    Default: Extended Log Field
  • None (in_mol_field) type: Field Type: Chem.Mol:
  • Intra-molecular energy field (intra_ene_field) type: Field Type: Float: Total intermolecular energy of the conformer
    Default: Intra-molecular energy
  • ln Qrot field (ln_qrot_field) type: Field Type: Float: Natural logarithm of the conformer rotational partition function
    Default: ln Qrot
  • ln Qvib field (ln_qvib_field) type: Field Type: Float: Natural logarithm of the conformer vibrational partition function
    Default: ln Qvib
  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field
  • None (out_mol_field) type: Field Type: Chem.Mol:
  • Probability of state field (prob_field) type: Field Type: Float: Probability of state associated with the conformer
    Default: Probability of state
  • Relative energy field (rel_ene_field) type: Field Type: Float: Relative energy of the conformer with respect to the lowest energy conformer of the ensemble
    Default: Relative energy
  • Relative lnQ field (rel_lnq_field) type: 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 (rot_ent_field) type: Field Type: Float: Rotational entropy of the conformer
    Default: Rotational Entropy
  • Solvation energy field (solv_ene_field) type: Field Type: Float: Solvation energy of the conformer
    Default: Solvation energy
  • Total energy field (tot_ene_field) type: Field Type: Float: Total (intramolecular + solvation) energy of the conformer
    Default: Total energy
  • Vibrational Entropy field (vib_ent_field) type: Field Type: Float: Vibrational entropy of the conformer
    Default: Vibrational Entropy

Hardware Parameters

Machine hardware requirements
  • Memory (MiB) (memory_mb) type: 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
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • Max Backlog Wait (max_backlog_wait) type: integer: The max time (in seconds) that a cube will be backlogged on a group before being re-evaluated
    Default: 600 , Min: 300
  • Temporary Disk Space (MiB) (disk_space) type: 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 (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”

Metrics Parameters

Cube Metric Parameters
  • Metric Period (None) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Cube Metrics (None) type: 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 (item_count) type: integer: The maximum number of messages to bundle together for a parallel cube.
    Default: 1 , Min: 1, Max: 65535
  • Maximum Failures (max_failures) type: integer: The maximum number of times to attempt processing a work item
    Default: 10 , Min: 1, Max: 100
  • Autoscale this Cube (autoscale) type: boolean: If True, let Orion manage the parallelism of this Cube
    Default: True
  • Maximum number of Cubes (max_parallel) type: integer: The maximum number of concurrently running copies of this Cube
    Default: 1000 , Min: 1
  • Minimum number of Cubes (min_parallel) type: integer: The minimum number of concurrently running copies of this Cube
    Default: 0