AD gromacs-protein-analysis
蛋白质分子动力学模拟分析的流程知识指南。当 Agent 需要执行某个分析但不清楚具体流程时调用。涵盖九种核心分析的完整工作流：(1) PBC 修正 - 消除周期性边界伪影，居中蛋白质/配体；(2) RMSD 分析 - 测量结构稳定性和模拟收敛性；(3) RMSF 分析 - 评估每个残基的灵活性；(4) 回转半径分析 - 评估蛋白质紧密性和折叠状态；(5) SASA 分析 - 研究溶剂可及性和表面性质；(6) DCCM 分析 - 动态互相关矩阵，研究原子间相关运动；(7) RDCM 分析 - 残基距离接触矩阵，分析残基间空间关系；(8) PCA 分析 - 主成分分析，识别集体运动和构象变化；(9) FEL 分析 - 自由能景观映射，使用 RMSD/Gyrate 或 PCA 作为反应坐标。包含分析间的依赖关系说明（如 FEL 依赖 PCA 或 RMSD/Gyrate 结果）。
As a process D 48/100 · Unfinished process — weak spots: result and completion, when it triggers, inputs and preconditions
How to improve
- Say in the description WHEN to use the skill ("use when…", example requests): that is the agent's main cue.
- Your own cases (evals/evals.json, 4–6 real requests with expected answers): the full check would then run those instead of a model-drafted suite.
- A spec.yaml with trigger phrases and assertions — a behaviour contract for CI; `skilltest init` writes a template.
Guard findings · 0
✓ No critical or high findings
Files scanned: 11. Evidence is masked. Grey chips explain why severity was lowered.
Against the Agent Skills spec
- warning
description-no-whendescription does not say WHEN to use the skill (no "use when")
Process rating: all ten parameters 48/100
- 0Result and completion. Does not say what the result is
- 0Inputs and preconditions. Does not say what the process needs to start
- 0Failures and branches. Linear process with no failure handling
- 20When it triggers. No condition that starts the skill
- 60Tools and files. Uses tools (bash) that frontmatter does not declare
- 100Steps. 61 steps
- 100Consistency. Name and required fields are in place
- 100Execution cost. Instruction body is 1636 tokens
- 100Running it twice. No mutating operations
- 100Progress reporting. Reports progress
- low 10 top-level sections: this looks like several domains in one skill
Everything here is measured from the skill text rather than judged by a model, so the numbers are checkable. A parameter weighs more when it is a more common reason for the process to stall.
Quality signals
- +5Description has no quoted example phrases that should trigger the skill
- +4Description does not say when NOT to use the skill (false activations)
- +3Output format is not stated: the model decides each time
- +1No license
- +2Single-language instructions
- +3Description length 391: enough signal without eating the budget
- +4Structure: 34 headings
- +3Step-by-step instructions: 61 items
- +4Has examples (1 code blocks)
- +4Reference files are cited in the instructions (9 of 9)
Quality base 70; lint remarks subtract, signals add up to 100. Result: 76.