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.
- center (boolean) : Center the system to the OpenMM unit cellDefault: 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. Not currently implemented in Gromacs | Default: “”
- hmr (boolean) : On enables Hydrogen Mass Repartitioning. Not currently implemented in GromacsDefault: True
- implicit_solvent (string) : Implicit Solvent Model. Not Currently implemented in GromacsDefault: NoneChoices: None, HCT, OBC1, OBC2, GBn, GBn2
- md_engine (string) : Select the MD available engineDefault: OpenMMChoices: OpenMM, Gromacs
- nonbondedCutoff (decimal) : The non-bonded cutoff in angstroms.
This is ignored if non-bonded method is NoCutoff | Default: 10
- pressure (decimal) : Pressure (atm)Default: 1.0
- 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 systemDefault: 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 overwrittenDefault: False
- suffix (string) : Filename suffix for output simulation filesDefault: npt
- temperature (decimal) : Temperature (Kelvin)Default: 300.0
- time (decimal) : NPT simulation time in nanosecondsDefault: 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 verbosityDefault: True
Cube Metric Parameters
- Metric Period (decimal) : How often to sample metrics, in secondsDefault: 60 Min: 1 Max: 300
- Cube Metrics (string) : Set of metrics to be collectedChoices: cpu, disk, memory, network
Machine hardware requirements
- Memory (MB) (decimal) : The minimum amount of memory this cube requires in MBsDefault: 1800 Min: 256.0 Max: 8589934592
- Temporary Disk Space (MB) (decimal) : The amount of disk space this cube requires in MBsDefault: 5120.0 Min: 128.0 Max: 8589934592
- GPUs (integer) : The number of GPUs to run this cube withDefault: 0 Max: 16
- CPUs (integer) : The number of CPUs to run this cube withDefault: 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 instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required
- Instance Tags (string) : Only run on machines with matching tags (comma separated)Default: “”
Parallel NPT 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 itemDefault: 10 Min: 1 Max: 100
- Autoscale this Cube (boolean) : If True, let Orion manage the parallelism of this CubeDefault: True
- Maximum number of Cubes (integer) : The maximum number of concurrently running copies of this CubeDefault: 1000 Min: 1
- Minimum number of Cubes (integer) : The minimum number of concurrently running copies of this CubeDefault: 0