Minimization Cube

This Cube performs energy minimization on the provided system. The system must have been parametrized by the Force Field cube and the system Parmed object must be present on the input record. In addition, a system identification number must be present on the input record as well. This can be accomplished by using the “ID Setting Cube”. The system minimization is performed by the selected MD engine, currently OpenMM and Gromacs only. Restraints and constraints can be used as well. Currently implicit solvent models can be used in OpenMM only. The cube requires a record as input and produces a new record with the minimized system.

Related Cubes

Calculation Parameters

  • None (center) type: boolean: Center the system to the OpenMM and Gromacs unit cell
    Default: True
  • None (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
  • None (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
  • 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
  • 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
  • None (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
  • None (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 restrain the system
    Default: True
  • None (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
  • None (steps) type: integer: Number of minimization steps. If 0 the minimization will continue until convergence
    Default: 2000
  • None (suffix) type: string: Filename suffix for output simulation files
    Default: min
  • None (temperature) type: decimal: Temperature (Kelvin)
    Default: 300
  • None (tolerance) type: decimal: Force tolerance in kJ/(mol nm). Minimization will be halted once the RMS of all force components reaches this tolerance.
    Default: 10.0
  • None (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
  • 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 Minimization Cube

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