Trajectory Poisson-Boltzmann and Surface Area Energies

Protein-ligand interaction solvation energies are calculated on an existing MD trajectory. The trajectory is taken from pre-existing protein and ligand trajectory OEMols. The Poisson-Boltzmann and Surface Area methods in the OEZap toolkits are used. The various energy components associated with the Poisson-Boltzmann and Surface Area energies are attached to the record as per-frame vectors of floats. The energy units are in kcal/mol.

Calculation Parameters

  • explicit_water (boolean) : Enable MMPBSA calculation with explicit water
    Default: False

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 Trajectory Poisson-Boltzmann and Surface Area Energies

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/TrjAnalysis/cubes.py