| name | molclaw-openawsem-tool |
| description | Runs OpenAWSEM simulations and extracts representative trajectory frames for downstream ensemble analysis. |
| license | MIT license |
| metadata | {"skill-author":"PJLab"} |
OpenAWSEM Simulation and Trajectory Extraction
Note:
- Local files are not directly accessible by the server. Please upload them to the server using
molclaw-file-transfer before execution.
- For PDB file inputs, it is recommended to preprocess them using
molclaw-pdbfixer before execution.
- Please refer to skill
molclaw-scp-server to complete tool invocation.
Usage
1. OpenAWSEM Simulation
The description of tool openawsem_sim.
Run OpenAWSEM coarse-grained protein simulation for annealing or NVT workflows in structure screening and folding studies.
Args:
sim_dir (str|None): Simulation directory containing *-openmmawsem.pdb or *_openmmawsem.pdb, default None.
pdb (str|None): PDB file path or PDB ID used by awsem_create when sim_dir is not provided, default None.
steps (float): Simulation step count, default 1e5.
mode (str): Temperature control mode in {annealing, nvt}, default annealing.
temperature (float): NVT temperature in Kelvin passed to source script argument --temperature, default 300.0.
platform (str): OpenMM platform in {CPU, CUDA, OpenCL}, default CPU.
use_frag_mem (bool): Whether to use fragment memory instead of single memory, default False.
compute_q (bool): Whether to enable Q-value related terms when available, default False.
dry_run (bool): Whether to validate setup without running MD steps, default False.
gpu_id (str): GPU device index for CUDA/OpenCL platform, default 0.
Return:
status (str): success, error, or partial_success execution status.
msg (str): Human-readable execution summary.
output_dir (str): Unique run directory under tool_result/openawsem_result.
simulation_dir (str): Effective simulation directory used by the delegated source script.
steps (float): Effective step count used in this run.
mode (str): Effective simulation mode used in this run.
temperature (float): Effective NVT temperature used in this run.
platform (str): Effective compute platform used in this run.
dry_run (bool): Effective dry-run flag used in this run.
output_files (dict): Key output file paths such as final PDB, energy log, checkpoint, and trajectory files.
metrics (dict): Parsed summary metrics such as energy log line count and last log line when available.
