NESGMX¶
This cubes runs the forward and reverse Bound and Unbound starting equilibrium frames by using Gromacs for each edge. The physical work associated with the edge mutations are calculated by using the Thermodynamic Integration method and saved on the record ready to be analyzed.
- Input
Data record Stream - Streamed-in of records containing Gromacs equilibrium frames data for the forward and reverse Bound and Unbound calculations
- Output
Data Record Stream - Streamed-out of records containing work data used to generate relative binding affinity data.
Calculation Parameters¶
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. Bonds2H means bonds with hydrogen are constrained, etc.Default: All-BondsChoices: None, Bonds2H, Angles2H, All-Bonds
CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 1 , Min: 1, Max: 128
Cube Metrics (cube_metrics) type: string: Set of metrics to be collectedChoices: 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
gmx_process_timeout (gmx_process_timeout) type: decimal: Gromacs process timeout in seconds (minimum value; increased per 50 ps of switch duration)Default: 3600.0
gmx_verbose (gmx_verbose) type: boolean: Enable GMX verbose modeDefault: False
GPUs (gpu_count) type: integer: The number of GPUs to run this cube withDefault: 0 , Max: 16
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
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 secondsDefault: 60Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPUDefault: 32
pressure (pressure) type: decimal: Pressure (atm)Default: 1.0
Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to addressDefault: 64
Spot policy (spot_policy) type: string: Control cube placement on spot market instancesDefault: ProhibitedChoices: Allowed, Preferred, NotPreferred, Prohibited, Required
suffix (suffix) type: string: Filename suffix for output simulation filesDefault: nes
temperature (temperature) type: decimal: Temperature (Kelvin)Default: 300.0
time (time) type: decimal: NPT simulation time in nanosecondsDefault: 0.05
Field parameters¶
Log Field (log_field) type: Field Type: String: The field to store messages to floe reportDefault: 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 addressDefault: 64
Thread limit per CPU (pids_per_cpu_limit) type: integer: The number of threads per CPUDefault: 32
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 withDefault: 0 , Max: 16
CPUs (cpu_count) type: integer: The number of CPUs to run this cube withDefault: 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 instancesDefault: ProhibitedChoices: 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 secondsDefault: 60Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
Cube Metrics (None) type: string: Set of metrics to be collectedChoices: cpu, disk, memory, network
Parallel NESGMX
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 itemDefault: 10 , Min: 1, Max: 100
Autoscale this Cube (autoscale) type: boolean: If True, let Orion manage the parallelism of this CubeDefault: True
Maximum number of Cubes (max_parallel) type: integer: The maximum number of concurrently running copies of this CubeDefault: 1000 , Min: 1
Minimum number of Cubes (min_parallel) type: integer: The minimum number of concurrently running copies of this CubeDefault: 0