NVT Cube

This cube performs MD simulation in the NVT 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 NVT 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.

Calculation Parameters

  • center (boolean) : Center the system to the OpenMM unit cell
    Default: False
  • constraints (string) : None, H-Bonds, H-Angles, 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: H-Bonds | Choices: None, H-Bonds, H-Angles, All-Bonds

  • freeze (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: “”

  • hmr (boolean) : On enables Hydrogen Mass Repartitioning. NOTE: Not currently implemented in Gromacs
    Default: False
  • implicit_solvent (string) : Implicit Solvent Model. NOTE:Not currently implemented in Gromacs
    Default: None
    Choices: None, HCT, OBC1, OBC2, GBn, GBn2
  • md_engine (string) : Select the MD available engine
    Default: OpenMM
    Choices: OpenMM, Gromacs
  • nonbondedCutoff (decimal) : The non-bonded cutoff in angstroms.

    This is ignored if non-bonded method is NoCutoff. | Default: 10

  • reporter_interval (decimal) : Time interval for reporting data in ns.

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

  • restraintWt (decimal) : Restraint weight for xyz atom restraints in kcal/(mol A^2)
    Default: 2.0
  • restraint_to_reference (boolean) : If True the starting reference system coordinates will be used to restraint the system
    Default: True
  • restraints (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 (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
  • suffix (string) : Filename suffix for output simulation files
    Default: nvt
  • temperature (decimal) : Temperature (Kelvin)
    Default: 300.0
  • time (decimal) : NVT simulation time in nanoseconds
    Default: 0.01
  • trajectory_interval (decimal) : Time interval for trajectory snapshots in ns.

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

  • verbose (boolean) : Increase log file verbosity
    Default: True

Metrics

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

Hardware Parameters

Machine hardware requirements

  • Memory (MB) (decimal) : The minimum amount of memory this cube requires in MBs
    Default: 1800 Min: 256.0 Max: 8589934592
  • Temporary Disk Space (MB) (decimal) : The amount of disk space this cube requires in MBs
    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: “”

Parallel NVT Cube

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: 100000
  • 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: MDOrion/MDEngines/cubes.py