NPT Cube

This Cube performs MD simulation in the NPT ensemble 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 NPT MD simulation 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 time evolved system. The total sampling time can be set by using the “time” cube parameter while the trajectory snapshots can be set by using the “trajectory_interval” cube parameter.

Related Cubes

Calculation Parameters

  • center (center) type: boolean: Center the system to the OpenMM unit cell
    Default: False
  • 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. HBonds 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. 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: True
  • Implicit Solvent (implicit_solvent) type: string: Implicit Solvent Model. 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
  • nonbondedCutoff (nonbondedCutoff) type: decimal: The non-bonded cutoff in angstroms.

    This is ignored if 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
  • pressure (pressure) type: decimal: Pressure (atm)
    Default: 1.0
  • Reporter interval (reporter_interval) type: decimal: Time interval for reporting data in ns.

    If 0 the reporter file will not be generated | Default: 0.0

  • restraintWt (restraintWt) type: decimal: Restraint weight for xyz atom restraints in kcal/(mol A^2)
    Default: 2.0
  • 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: False
  • 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
  • suffix (suffix) type: string: Filename suffix for output simulation files
    Default: npt
  • temperature (temperature) type: decimal: Temperature (Kelvin)
    Default: 300.0
  • time (time) type: decimal: NPT simulation time in nanoseconds
    Default: 0.01
  • Trajectory frames (trajectory_frames) type: integer: The total number of trajectory frames. If it is set to zero and the trajectory interval parameter is set to zero no trajectory is generated. If it is different from zero and the trajectory interval parameter is set to zero the produced trajectory will have the selected number of frames. If different from zero and the trajectory interval parameter is different from zero the total number of generated frames will be calculated by just using the trajectory interval and the md time step (2fs and 4fs hmr on)
    Default: 0
  • Trajectory interval (trajectory_interval) type: decimal: Time interval for trajectory snapshots in ns.

    If 0 the trajectory file will not be generated | Default: 0.0

  • 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
  • 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 NPT 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