Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add dtunai/agent-skills-for-compute --skill biosimspacegit clone --depth 1 https://github.com/dtunai/agent-skills-for-computeWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/dtunai/agent-skills-for-compute/biosimspace)<a href="https://agentmods.dev/skills/dtunai/agent-skills-for-compute/biosimspace"><img src="https://agentmods.dev/badge/skills/dtunai/agent-skills-for-compute/biosimspace/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/dtunai/agent-skills-for-compute/biosimspace"><img src="https://agentmods.dev/badge/skills/dtunai/agent-skills-for-compute/biosimspace.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00059 | $0.03175 |
| Opus 5.5 | $0.00024 | $0.01270 |
| Sonnet 5.5 | $0.00012 | $0.00635 |
| Haiku 4.5 | $0.00006 | $0.00317 |
Grade A, and why
biosimspace scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 370 lines — stays where its author put it; the contents beside it link to each section on GitHub.
BioSimSpace
Engine-agnostic Python framework for biomolecular simulation. Write portable workflows once — BioSimSpace translates to AMBER, GROMACS, NAMD, OpenMM, or SOMD at runtime.
Official Sources:
Quick Start
# Install via conda (recommended)
conda create -n openbiosim -c conda-forge -c openbiosim biosimspace
conda activate openbiosim
# Optional: install MD engines
conda install -c conda-forge ambertools gromacs
import BioSimSpace as BSS
Architecture
| Module | Purpose |
|---|---|
BSS.IO |
Read/write molecules (PDB, MOL2, GRO, PRM7, RST7, SDF, DCD...) |
BSS.Parameters |
Parameterise with force fields (ff14SB, GAFF, GAFF2, OpenFF...) |
BSS.Solvent |
Solvate in water boxes (TIP3P, SPC/E, TIP4P, OPC...) |
BSS.Protocol |
Engine-agnostic simulation protocols |
BSS.Process |
Engine-specific process drivers (Amber, Gromacs, Namd, OpenMM, Somd) |
BSS.MD |
Auto-select engine and run |
BSS.FreeEnergy |
Relative FEP and ATM (alchemical transfer method) |
BSS.Align |
Atom mapping, alignment, merging for FEP |
BSS.Metadynamics |
Enhanced sampling via PLUMED |
BSS.Convert |
Convert between BSS, RDKit, OpenMM, Sire representations |
BSS.Box |
Simulation box generators (cubic, rhombic dodecahedron, truncated octahedron) |
BSS.Types |
Physical quantities (Length, Temperature, Time, Energy, Pressure...) |
BSS.Units |
Unit constants (BSS.Units.Length.nanometer, etc.) |
BSS.Gateway |
Node I/O for reusable workflow components |
BSS.Notebook |
Visualization (plots, 3D views via NGLView) |
BSS.Trajectory |
Trajectory analysis wrapper |
BSS.Stream |
Serialization/checkpointing |
Supported Engines
| Engine | Process Class | Detection |
|---|---|---|
| AMBER | BSS.Process.Amber |
AMBERHOME env var |
| GROMACS | BSS.Process.Gromacs |
gmx/gmx_mpi in PATH or GROMACSHOME |
| NAMD | BSS.Process.Namd |
namd2/namd3 in PATH |
| OpenMM | BSS.Process.OpenMM |
Python import |
| SOMD | BSS.Process.Somd |
Part of Sire/OpenBioSim stack |
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 2mo ago First seen · 370 lines · 59 tokens per session scan A 295bb5204322
biosimspace is a skill published in the GitHub repository dtunai/agent-skills-for-compute (2 stars, last pushed 7mo ago), licensed MIT. It adds 59 tokens to every session and 3,175 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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