T03 · Remote Payload Retrieval and Execution
Error
- Location
references/tools/INSTALLATION.md:219- Finding
Unverified Remote Python Payload Downloaded and Installed as a System Command
- Content
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- Remediation
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Security audit
Automd Gromacs
Security checks for vulnerabilities and agentic risk
Overview
This GROMACS automation skill is mostly coherent, but it includes unsafe installation and troubleshooting instructions that can install unverified code globally or weaken the host environment.
Review commands before letting an agent run them. Prefer a fresh conda environment or disposable container, preinstall pinned dependencies yourself, avoid AUTOMD_AUTO_INSTALL and AUTOMD_CG_ALLOW_DOWNLOAD unless you trust the sources, do not install downloaded scripts into /usr/local/bin without verifying them, and avoid persistent ~/.bashrc or Docker capability changes unless you understand the host impact.
Vulnerability Patterns
- Remote Payload Retrieval and ExecutionFetches external code whose behavior can change after review
- System PersistenceInstalls backdoors, hooks, services, or scheduled tasks that survive the run
- Tool Hijacking and SpoofingModifies or replaces tools so legitimate-looking calls execute attacker logic
- Insecure DependenciesIntroduces malicious components through unsafe dependency sources
- Skill Instruction HijackingAlters the agent's session goals or safety constraints when the skill loads
Findings (6)
T08 · Insecure Dependencies
Error
- Location
references/tools/INSTALLATION.md:52- Finding
Unpinned Git Repository Code Is Installed or Enabled for Execution
- Content
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- Remediation
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T08 · Insecure Dependencies
Error
- Location
scripts/advanced/freeenergy.sh:10- Finding
Opt-In Runtime Dependency Installation Executes Unpinned Packages
- Content
View full analysis
/dev/null; then missing="$missing $tool" fi done if [[ -n "$missing" ]]; then echo "[MISSING] Missing tools:$missing" return 1 fi return 0 fi for tool in "${tools[@]}"; do if ! command -v "$tool" &> /dev/null; then if command -v conda &> /dev/null; then conda install -c conda-forge "$tool" -y &> /dev/null && installed=1 elif command -v pip &> /dev/null; then pip install "$tool" &> /dev/null && installed=1 fi if [ $installed -eq 1 ]; then echo "[SUCCESS] $tool installed" else return 1 fi fi done return 0 } ``` From `scripts/advanced/coarse-grained.sh:173-189`: ```bash if [[ "${AUTOMD_AUTO_INSTALL:-0}" != "1" ]]; then error "martinize not available — install it or set AUTOMD_AUTO_INSTALL=1" fi if command -v pip3 &> /dev/null; then pip3 install vermouth-martinize 2>&1 | tail -5 || { error "martinize unavailable" } fi ``` ### Technical Analysis When `AUTOMD_AUTO_INSTALL=1`, simulation scripts install packages dynamically from Conda or pip without exact version constraints, package hashes, a lockfile, or mandatory environment isolation. Package installation can execute build backends, setup hooks, native compilation steps, and transitive dependencies. ...[truncated 1265 chars]- Remediation
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T08 · Insecure Dependencies
Warning
- Location
scripts/advanced/coarse-grained.sh:106- Finding
Downloaded Force-Field Archives Are Extracted Without Integrity or Path Validation
- Content
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/dev/null; then wget -q https://cgmartini.nl/images/parameters/martini_v3.0.0/martini_v3.0.0.tar.gz -O martini3.tar.gz || { error "MARTINI 3 force field unavailable" } tar -xzf martini3.tar.gz rm martini3.tar.gz fi else if command -v wget &> /dev/null; then wget -q https://cgmartini.nl/images/parameters/martini_v2.2/martini_v2.2.tar.gz -O martini2.tar.gz || { error "MARTINI 2 force field unavailable" } tar -xzf martini2.tar.gz rm martini2.tar.gz fi fi ``` ### Technical Analysis When `AUTOMD_CG_ALLOW_DOWNLOAD=1`, the script downloads a remote tar archive and immediately extracts it. HTTPS protects the connection against ordinary passive interception, but the script does not verify an expected checksum or signature and therefore cannot detect a compromised origin or altered upstream artifact. The script also does not inspect archive member paths before extraction. A malicious archive could contain absolute paths, `../` traversal components, symbolic links, or files designed to overwrite existing content writable by the current user. Even when no executable payload is present, altered force-field data can silently change scientific calculations and invalidate results. ### Attack Path 1. A user enables automatic coarse-grained force-field downloads. 2. The hosting origin or its distribution infrastructure is compromised. 3. The server provides a modified archive. 4. The workflow downloads the archive under a fixed local filename. 5. `tar -xzf` extracts all members without checking their paths or integrity. 6. Crafted members overwrite accessible files, or modified force-fiel ...[truncated 580 chars]- Remediation
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T07 · Tool Hijacking and Spoofing
Error
- Location
references/gpu/gpu-installation.md:27- Finding
Unverified CMake Binary Is Installed Into the Global Command Path
- Content
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- Remediation
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T06 · System Persistence
Warning
- Location
references/gpu/gpu-installation.md:122- Finding
GPU Installation Instructions Persistently Modify Shell Startup Configuration
- Content
View full analysis
/opt/gromacs-2025.4-gpu/env.sh << 'EOF' export GMX=/opt/gromacs-2025.4-gpu export PATH=$GMX/bin:$PATH export LD_LIBRARY_PATH=$GMX/lib64:$LD_LIBRARY_PATH export CUDA_HOME=/usr/local/cuda-12.8 export PATH=$CUDA_HOME/bin:$PATH export LD_LIBRARY_PATH=$CUDA_HOME/lib64:$LD_LIBRARY_PATH EOF echo 'source /opt/gromacs-2025.4-gpu/env.sh' >> ~/.bashrc source /opt/gromacs-2025.4-gpu/env.sh gmx --version 2>&1 | grep -iE "GPU|CUDA|SIMD" ``` ### Technical Analysis The installation guide appends a `source` command to `~/.bashrc`, causing `/opt/gromacs-2025.4-gpu/env.sh` to run in every future interactive Bash session. This is cross-session persistence and is not required to complete a single GROMACS build or simulation. The sourced script modifies `PATH` and `LD_LIBRARY_PATH`, which influence executable and shared-library resolution. If the `/opt` installation or environment script is later replaced, every new shell can be redirected to attacker-controlled commands or libraries. Repeated execution also appends duplicate entries because the command does not check whether the line already exists. ### Attack Path 1. A user follows the GPU installation instructions. 2. The persistent `source` directive is appended to `~/.bashrc`. 3. An attacker who can later modify the `/opt` environment script, GROMACS binary directory, or referenced libraries changes their contents. 4. The user starts a new Bash session. 5. Bash automatically sources the modified script. 6. The attacker-controlled path or library configuration affects commands run in that and subsequent sessions. ### Impact Assessment The startup hook executes with the privileges of the affected user on every interactive Bash session. A compromised environment script can run arbitrary shell commands, ...[truncated 285 chars]- Remediation
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Vulnerability Patterns
- Privilege EscalationExcessive Permissions, Sudo/Root Execution, Credential Access
- Tool MisuseTool Parameter Abuse, Chaining Abuse, Unsafe Defaults
- YARA SignaturesMalware Match, Webshell Match, Cryptominer Match
- MCP Tool PoisoningHidden Instructions, Unicode Deception, Parameter Description Injection
- Prompt InjectionInstruction Override, Hidden Instructions, Exfiltration Commands
Findings (171)
Tp4
High
- Category
- MCP Tool Poisoning
- Confidence
- 88% confidence
- Finding
The description presents a broad AutoMD-GROMACS skill with workflow automation plus enhanced sampling, special-system simulation, advanced analysis, publication-ready visualization, troubleshooting, and token optimization. The supplied code chunk only implements a single ligand–protein simulation pipeline in Bash. It does include some troubleshooting-oriented behavior (error messages, fallback ligand parameterization, optional dependency auto-install), so that part partially aligns. However, the main mismatch is that the declared purpose is substantially broader than the actual behavior shown. Additionally, the code has an undeclared capability to install packages at runtime via conda or pip when AUTOMD_AUTO_INSTALL=1, which is a meaningful side effect not reflected in the declared permissions/capabilities. The report it generates contains analysis and visualization instructions, but does not actually perform advanced analysis or produce publication-ready visualizations. Therefore the description does not accurately represent this specific code chunk.
- Content
Tp4
High
- Category
- MCP Tool Poisoning
- Confidence
- 93% confidence
- Finding
The code is related to the declared domain of molecular dynamics automation for GROMACS, so it is not wholly unrelated. However, the supplied chunk implements a much narrower capability than the description claims. It handles one specialized membrane-protein setup/equilibration pipeline and basic report generation. It does not implement enhanced sampling methods, substantive advanced analysis, publication-ready visualization generation, or any clearly AI-facing/token-optimization features. The script does include limited troubleshooting-style behavior through dependency checks, optional auto-install, and error messages, and it fits 'special-system simulation' in the membrane-protein sense. Still, the declared description overstates the capabilities actually present in this code chunk, so this should be flagged as a description-behavior mismatch.
- Content
Tp4
High
- Category
- MCP Tool Poisoning
- Confidence
- 94% confidence
- Finding
The supplied code chunk does fit part of the declared purpose: it is an automation workflow for GROMACS and is AI-friendly in the sense of structured steps and concise error messages. However, the description substantially overstates the implemented capabilities in this chunk. The script only orchestrates a standard six-step MD pipeline and basic analysis via other scripts. There is no evidence here of enhanced sampling methods, special-system simulation support, advanced analysis, or publication-ready visualization. Troubleshooting is limited to basic dependency/input checks and fixed error hints, not robust built-in troubleshooting. This is not a harmful undeclared capability issue; rather, the declared description is materially broader than the observed behavior, so it should be flagged as a description/behavior mismatch.
- Content
Tp4
High
- Category
- MCP Tool Poisoning
- Confidence
- 94% confidence
- Finding
The description presents a comprehensive AutoMD-GROMACS system for end-to-end molecular dynamics automation, including workflow management, enhanced sampling, special-system simulation, advanced analysis, visualization, and troubleshooting. The supplied code chunk is much narrower: it is a basic analysis script for existing GROMACS outputs (
md.tpr,md.xtc). It preprocesses trajectories and runs standard analyses (RMSD, RMSF, gyration radius, hydrogen bonds, SASA, optional DSSP), computes simple summary statistics, and writes a Markdown report. There is some built-in troubleshooting via checks and error messages, so that aspect is partially consistent. However, the code does not implement simulation workflow orchestration, enhanced sampling, special-system handling, advanced analysis beyond standard metrics, or publication-ready visualization. Therefore the declared description materially overstates the behavior of this code chunk.- Content
Tp4
High
- Category
- MCP Tool Poisoning
- Confidence
- 94% confidence
- Finding
The supplied code chunk is narrowly focused on preparing a standard GROMACS system from a PDB through topology generation, boxing, solvation, ion addition, energy minimization, and report generation. It does include basic troubleshooting/error messages and a small amount of automatic parameter selection, which partially aligns with 'automation' and 'built-in troubleshooting.' However, the declared description promises a much broader platform: enhanced sampling, special-system simulation, advanced analysis, publication-ready visualization, and wider workflow orchestration. None of those capabilities are present in this code chunk. The primary purpose of the code is initial system setup, not the full-featured molecular dynamics automation suite described. Therefore the description materially overstates what this code actually does.
- Content
Tp4
High
- Category
- MCP Tool Poisoning
- Confidence
- 95% confidence
- Finding
The declared description presents a comprehensive molecular dynamics automation system with workflow orchestration, enhanced sampling, simulation support, advanced analysis, visualization, and troubleshooting. The supplied code does not implement those broad capabilities. It only parses CLI flags, checks for
gmx, validates an input file, and dispatches to a few basic GROMACS commands (trjconv,make_ndx) for convert/center/fit/PBC/index tasks. There is no evidence here of workflow automation, simulation setup/execution, enhanced sampling, special-system handling, advanced analysis, or publication-ready visualization. This is therefore a description-to-behavior mismatch due to substantial overstatement of the implemented functionality in the provided code chunk.- Content
Tp4
High
- Category
- MCP Tool Poisoning
- Confidence
- 97% confidence
- Finding
The description claims a comprehensive AutoMD-GROMACS system with broad MD workflow automation, enhanced sampling, special simulations, analysis, visualization, and troubleshooting. The supplied code chunk is only a simple Bash utility wrapper around standard GROMACS commands for preprocessing and trajectory manipulation. While it is related to GROMACS and molecular dynamics, it does not implement most of the declared headline capabilities. This is a material description-to-behavior mismatch due to substantial overstatement of functionality.
- Content
Credential Access
High
- Category
- Privilege Escalation
- Confidence
- 70% confidence
- Finding
Code accesses credential files (SSH keys, AWS credentials, etc.). This could indicate credential theft attempts.
- Content
全新安装 (Ubuntu 22.04+)
bash # 安装 NVIDIA CUDA keyring wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.1-1_all.deb dpkg -i cuda-keyring_1.1-1_all.deb apt-get update
Credential Access
High
- Category
- Privilege Escalation
- Confidence
- 70% confidence
- Finding
Code accesses credential files (SSH keys, AWS credentials, etc.). This could indicate credential theft attempts.
- Content
全新安装 (Ubuntu 22.04+)
bash # 安装 NVIDIA CUDA keyring wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.1-1_all.deb dpkg -i cuda-keyring_1.1-1_all.deb apt-get update
Credential Access
High
- Category
- Privilege Escalation
- Confidence
- 70% confidence
- Finding
Code accesses credential files (SSH keys, AWS credentials, etc.). This could indicate credential theft attempts.
- Content
全新安装 (Ubuntu 22.04+)
bash # 安装 NVIDIA CUDA keyring wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.1-1_all.deb dpkg -i cuda-keyring_1.1-1_all.deb apt-get update
YARA rule 'backdoor_persistence': Backdoor persistence with malicious payloads (shell commands, SSH key injection, hidden root users) [malware]
High
- Category
- YARA Match
- Confidence
- 75% confidence
- Finding
YARA rule matched a known malware signature (reverse shell, backdoor, ransomware, C2 framework, or info stealer).
- Content
�心数
make install
text ## 环境配置 ```bash # 创建环境脚本 cat > /opt/gromacs-2025.4-gpu/env.sh << 'EOF' export GMX=/opt/gromacs-2025.4-gpu export PATH=$GMX/bin:$PATH export LD_LIBRARY_PATH=$GMX/lib64:$LD_LIBRARY_PATH export CUDA_HOME=/usr/local/cuda-12.8 export PATH=$CUDA_HOME/bin:$PATH export LD_LIBRARY_PATH=$CUDA_HOME/lib64:$LD_LIBRARY_PATH EOF # 自动加载（写入 .bashrc） echo 'source /opt/gromacs-2025.4-gpu/env.sh' >> ~/.bashrc验证
bash source /opt/gromacs-2025.4-gpu/env.sh gmx --version 2>&1 | grep -iE "GPU|CUDA|SIMD"期望输出：
text GPU support: CUDA SIMD instructions: AVX2_256 GPU FFT library: cuFFT CUDA compiler: /usr/local/cuda-12.8/bin/nvccCUDA 架构对照表
GPU 系列 架构 CMAKE_CUDA_ARCHITECTURES RTX 5090/5080/5070/5060 Blackwell 120RTX 4090/4080/4070/4060 Ada Lovelace 89RTX 3090/3080/3070 Ampere 86A100/H10
Privileged Container / Container Escape
High
- Category
- Privilege Escalation
- Confidence
- 97% confidence
- Finding
Advising the addition of
SYS_PTRACEto a container grants powerful debugging and process-inspection capability that is unnecessary for most molecular dynamics workflows. In the context of untrusted or broadly scoped containers, this increases the risk of sensitive process inspection, bypass of hardening assumptions, and greater impact from a compromised image.- Content
不在 /etc/hosts 中会导致 OpenMPI 进程间无法通信。 在物理机/共享集群上，不应修改 /etc/hosts，应联系系统管理员配置域名解析。
Fix 3: Docker 容器需要 --cap-add=SYS_PTRACE
⚠️
SYS_PTRACE是 Linux security capability，授予容器进程 ptrace 权限。仅信任的容器镜像使用。 如果在容器内完成 Fix 1+2 后 mpirun 仍卡死：bash
Privileged Container / Container Escape
High
- Category
- Privilege Escalation
- Confidence
- 98% confidence
- Finding
The explicit
docker run --cap-add=SYS_PTRACE ...command operationalizes a privileged container configuration that weakens container isolation. Because this is a copy-paste-ready command in troubleshooting documentation, it materially increases the chance that users will grant elevated capabilities without fully understanding the security consequences.- Content
text **需要容器管理员**在启动时添加： ```bash docker run --cap-add=SYS_PTRACE ...如果无法修改容器权限，只能使用单核模式 (
%pal nprocs 1 end)
Tool Parameter Abuse
High
- Category
- Tool Misuse
- Confidence
- 91% confidence
- Finding
The documentation instructs users to run
rm -rf output/*, which is a destructive filesystem operation. While the path is not obviously attacker-controlled in this snippet, blindly recommending recursive deletion can cause unintended data loss if executed from the wrong directory, ifoutputis a symlink, or if users adapt the command unsafely in automation.- Content
重新生成拓扑:
bash # 从头开始 rm -rf output/* ./setup.sh --input protein.pdb --output output
Sudo/Root Execution
Medium
- Category
- Privilege Escalation
- Confidence
- 70% confidence
- Finding
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
- Content
md - **INSTALLATION.md warnings** — security advisories added before all `sudo`, `/etc/`, and system-level operations; `insane.py` download uses HTTPS; `~/.gromacs_env.sh` warns against adding to `.bashrc` - **ligand-topology.md warnings** — `apt-get`, `/etc/ld.so.conf.d/`, and `ldconfig` commands now commented out with security advisories and conda alternatives - **qmmm-errors.md warnings** — `/etc/hosts` modification now includes security context and container-only guidance; `SYS_PTRACE` capability risk documented - **membrane-errors.md warnings** — `sudo mv insane.py` replaced with user-path `~/.local/bin/` install; HTTPS download ## [5.3.2] - 2026-06-01
Sudo/Root Execution
Medium
- Category
- Privilege Escalation
- Confidence
- 70% confidence
- Finding
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
- Content
md - **INSTALLATION.md warnings** — security advisories added before all `sudo`, `/etc/`, and system-level operations; `insane.py` download uses HTTPS; `~/.gromacs_env.sh` warns against adding to `.bashrc` - **ligand-topology.md warnings** — `apt-get`, `/etc/ld.so.conf.d/`, and `ldconfig` commands now commented out with security advisories and conda alternatives - **qmmm-errors.md warnings** — `/etc/hosts` modification now includes security context and container-only guidance; `SYS_PTRACE` capability risk documented - **membrane-errors.md warnings** — `sudo mv insane.py` replaced with user-path `~/.local/bin/` install; HTTPS download ## [5.3.2] - 2026-06-01
Sudo/Root Execution
Medium
- Category
- Privilege Escalation
- Confidence
- 70% confidence
- Finding
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
- Content
md - **INSTALLATION.md warnings** — security advisories added before all `sudo`, `/etc/`, and system-level operations; `insane.py` download uses HTTPS; `~/.gromacs_env.sh` warns against adding to `.bashrc` - **ligand-topology.md warnings** — `apt-get`, `/etc/ld.so.conf.d/`, and `ldconfig` commands now commented out with security advisories and conda alternatives - **qmmm-errors.md warnings** — `/etc/hosts` modification now includes security context and container-only guidance; `SYS_PTRACE` capability risk documented - **membrane-errors.md warnings** — `sudo mv insane.py` replaced with user-path `~/.local/bin/` install; HTTPS download ## [5.3.2] - 2026-06-01
Sudo/Root Execution
Medium
- Category
- Privilege Escalation
- Confidence
- 70% confidence
- Finding
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
- Content
md - **INSTALLATION.md warnings** — security advisories added before all `sudo`, `/etc/`, and system-level operations; `insane.py` download uses HTTPS; `~/.gromacs_env.sh` warns against adding to `.bashrc` - **ligand-topology.md warnings** — `apt-get`, `/etc/ld.so.conf.d/`, and `ldconfig` commands now commented out with security advisories and conda alternatives - **qmmm-errors.md warnings** — `/etc/hosts` modification now includes security context and container-only guidance; `SYS_PTRACE` capability risk documented - **membrane-errors.md warnings** — `sudo mv insane.py` replaced with user-path `~/.local/bin/` install; HTTPS download ## [5.3.2] - 2026-06-01
Sudo/Root Execution
Medium
- Category
- Privilege Escalation
- Confidence
- 70% confidence
- Finding
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
- Content
md - **INSTALLATION.md warnings** — security advisories added before all `sudo`, `/etc/`, and system-level operations; `insane.py` download uses HTTPS; `~/.gromacs_env.sh` warns against adding to `.bashrc` - **ligand-topology.md warnings** — `apt-get`, `/etc/ld.so.conf.d/`, and `ldconfig` commands now commented out with security advisories and conda alternatives - **qmmm-errors.md warnings** — `/etc/hosts` modification now includes security context and container-only guidance; `SYS_PTRACE` capability risk documented - **membrane-errors.md warnings** — `sudo mv insane.py` replaced with user-path `~/.local/bin/` install; HTTPS download ## [5.3.2] - 2026-06-01
Sudo/Root Execution
Medium
- Category
- Privilege Escalation
- Confidence
- 70% confidence
- Finding
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
- Content
md - **INSTALLATION.md warnings** — security advisories added before all `sudo`, `/etc/`, and system-level operations; `insane.py` download uses HTTPS; `~/.gromacs_env.sh` warns against adding to `.bashrc` - **ligand-topology.md warnings** — `apt-get`, `/etc/ld.so.conf.d/`, and `ldconfig` commands now commented out with security advisories and conda alternatives - **qmmm-errors.md warnings** — `/etc/hosts` modification now includes security context and container-only guidance; `SYS_PTRACE` capability risk documented - **membrane-errors.md warnings** — `sudo mv insane.py` replaced with user-path `~/.local/bin/` install; HTTPS download ## [5.3.2] - 2026-06-01
Sudo/Root Execution
Medium
- Category
- Privilege Escalation
- Confidence
- 70% confidence
- Finding
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
- Content
md - **INSTALLATION.md warnings** — security advisories added before all `sudo`, `/etc/`, and system-level operations; `insane.py` download uses HTTPS; `~/.gromacs_env.sh` warns against adding to `.bashrc` - **ligand-topology.md warnings** — `apt-get`, `/etc/ld.so.conf.d/`, and `ldconfig` commands now commented out with security advisories and conda alternatives - **qmmm-errors.md warnings** — `/etc/hosts` modification now includes security context and container-only guidance; `SYS_PTRACE` capability risk documented - **membrane-errors.md warnings** — `sudo mv insane.py` replaced with user-path `~/.local/bin/` install; HTTPS download ## [5.3.2] - 2026-06-01
Sudo/Root Execution
Medium
- Category
- Privilege Escalation
- Confidence
- 70% confidence
- Finding
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
- Content
sh - **INSTALLATION.md warnings** — security advisories added before all `sudo`, `/etc/`, and system-level operations; `insane.py` download uses HTTPS; `~/.gromacs_env.sh` warns against adding to `.bashrc` - **ligand-topology.md warnings** — `apt-get`, `/etc/ld.so.conf.d/`, and `ldconfig` commands now commented out with security advisories and conda alternatives - **qmmm-errors.md warnings** — `/etc/hosts` modification now includes security context and container-only guidance; `SYS_PTRACE` capability risk documented - **membrane-errors.md warnings** — `sudo mv insane.py` replaced with user-path `~/.local/bin/` install; HTTPS download ## [5.3.2] - 2026-06-01
Sudo/Root Execution
Medium
- Category
- Privilege Escalation
- Confidence
- 70% confidence
- Finding
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
- Content
sh - **INSTALLATION.md warnings** — security advisories added before all `sudo`, `/etc/`, and system-level operations; `insane.py` download uses HTTPS; `~/.gromacs_env.sh` warns against adding to `.bashrc` - **ligand-topology.md warnings** — `apt-get`, `/etc/ld.so.conf.d/`, and `ldconfig` commands now commented out with security advisories and conda alternatives - **qmmm-errors.md warnings** — `/etc/hosts` modification now includes security context and container-only guidance; `SYS_PTRACE` capability risk documented - **membrane-errors.md warnings** — `sudo mv insane.py` replaced with user-path `~/.local/bin/` install; HTTPS download ## [5.3.2] - 2026-06-01
Sudo/Root Execution
Medium
- Category
- Privilege Escalation
- Confidence
- 70% confidence
- Finding
Commands invoke sudo or root privileges. Verify this elevated access is necessary and justified.
- Content
sh - **INSTALLATION.md warnings** — security advisories added before all `sudo`, `/etc/`, and system-level operations; `insane.py` download uses HTTPS; `~/.gromacs_env.sh` warns against adding to `.bashrc` - **ligand-topology.md warnings** — `apt-get`, `/etc/ld.so.conf.d/`, and `ldconfig` commands now commented out with security advisories and conda alternatives - **qmmm-errors.md warnings** — `/etc/hosts` modification now includes security context and container-only guidance; `SYS_PTRACE` capability risk documented - **membrane-errors.md warnings** — `sudo mv insane.py` replaced with user-path `~/.local/bin/` install; HTTPS download ## [5.3.2] - 2026-06-01
Missing User Warnings
Medium
- Category
- Not specified by scanner
- Confidence
- 90% confidence
- Finding
The README gives direct commands to run setup, simulation, analysis, and visualization scripts but does not warn that these operations may consume substantial CPU/GPU time, require licensed or heavyweight scientific dependencies, and create or overwrite files in the working directory. In an AI-agent context, copy-pastable execution examples materially increase the chance of unintended expensive or destructive runs, especially when an agent may treat documentation examples as safe defaults.
- Content