NESGMXChimera¶
Relative Binding Free Energy calculations via Alchemical Transformations are usually done by using a chimeric molecule where the common scaffold between two ligands involved in an edge is modified to contain the atom excesses of the two edge ligands. This cube generates the chimera molecule and inject it on select frames from the Bound and Unbound simulations for the Gromacs forward and reverse Non Equilibrium simulations.
- Input
Data record Stream - Streamed-in of the Gathered Bound and Unbound simulation data
- Output
Data Record Stream - Streamed-out of records containing Gromacs forward and reverse Bound and Unbound data.
Calculation Parameters¶
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
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
lig_res_name (lig_res_name) type: string: The new ligand residue nameDefault: LIG
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
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
trajectory_frames (trajectory_frames) type: integer: The total number of trajectory frames to run NESDefault: 80
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 NESGMXChimera
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