Minimization Cube for IFD

This Cube performs multi-layered restrained energy minimization on the docked pose/reference receptor conformation.

Related Cubes

Calculation Parameters

  • center (center) type: boolean: Center the system to the OpenMM and Gromacs unit cell
    Default: True
  • constraints (constraints) type: string: None, Bonds2H, Angles2H, or All-Bonds Which type of constraints to add to the system. None means no bonds are constrained. Bonds2H means bonds with hydrogen are constrained, etc.
    Default: Bonds2H
    Choices: None, Bonds2H, Angles2H, All-Bonds
  • 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
  • freeze (freeze) type: string: Mask selection to freeze atoms along the MD simulation. Possible keywords are: ligand, protein, water, ions, ca_protein, cofactors. The selection can be refined by using logical tokens: not, noh, and, or, diff, around. NOTE: Not currently implemented in Gromacs.
    Default: “”
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • Hydrogen Mass Repartitioning (hmr) type: boolean: Give hydrogens more mass and increase the MD integration time step from 2 to 4 fs
    Default: False
  • Implicit solvent (implicit_solvent) type: string: Implicit Solvent Model. NOTE:Not currently implemented in Gromacs.
    Default: None
    Choices: None, HCT, OBC1, OBC2, GBn, GBn2
  • 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
  • MD engine (md_engine) type: string: Select the available MD engine
    Default: OpenMM
    Choices: OpenMM, Gromacs
  • 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
  • Minimization Type (min_type) type: string: Select minimization type. Induced Fit1 will relax active site side chain only w rstr, and Induced Fit2 will relax all wo rstr.
    Default: Default
    Choices: Default, Induced Fit1, Induced Fit2
  • nonbondedCutoff (nonbondedCutoff) type: decimal: The non-bonded cutoff in angstroms. This is ignored if the non-bonded method is NoCutoff
    Default: 10
  • Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPU
    Default: 32
  • restraint1Wt (restraint1Wt) type: decimal: (For Min Type:’Induced Fit1’ only) Restraint weight for the ligand in kcal/(mol A^2)
    Default: 2.0
  • restraint2Wt (restraint2Wt) type: decimal: (For Min Type:’Induced Fit1’ only) Restraint weight for the active site side chains in kcal/(mol A^2)
    Default: 0.2
  • restraint3Wt (restraint3Wt) type: decimal: (For Min Type:’Induced Fit1’ only) Restraint weight for the active site backbones in kcal/(mol A^2)
    Default: 1.0
  • restraint4Wt (restraint4Wt) type: decimal: (For Min Type:’Induced Fit1’ only) Restraint weight for the non-active site in kcal/(mol A^2)
    Default: 2.0
  • restraintWt (restraintWt) type: decimal: Restraint weight for xyz atom restraints in kcal/(mol A^2)
    Default: 5.0
  • Restraint to reference (restraint_to_reference) type: boolean: If True the starting reference system coordinates will be used to restraint the system
    Default: True
  • restraints (restraints) type: string: Mask selection to apply harmonic restraints. Possible keywords are: ligand, protein, water, ions, ca_protein, cofactors. The selection can be refined by using logical tokens: not, noh, and, or, diff, around.
    Default: “”
  • Save MD stage (save_md_stage) type: boolean: Save the MD simulation stage. If True the MD, simulation data will be appended to the md simulation stages otherwise the last MD stage will be overwritten
    Default: True
  • 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
  • steps (steps) type: integer: Number of minimization steps. If 0 the minimization will continue until convergence
    Default: 2000
  • suffix (suffix) type: string: Filename suffix for output simulation files
    Default: min
  • temperature (temperature) type: decimal: Temperature (Kelvin)
    Default: 300
  • tolerance (tolerance) type: decimal: tolerance parameter in kj/mol for OpenMM minimizeEnergy method
    Default: 10.0
  • verbose (verbose) type: boolean: Increase log file verbosity
    Default: True

Field parameters

  • Log Field (log_field) type: Field Type: String: The field to store messages to floe report
    Default: Log Field

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
  • 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 Minimization Cube for IFD

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