molecular-dynamics

Molecular Dynamics Simulation Pipeline

Autonomous molecular dynamics simulation from structure to analysis. Inspired by DynaMate's three-module architecture: Experiment Planner → Simulation Performer → Result Analyzer.

When to Use

• "帮我跑个 MD 模拟" or "molecular dynamics simulation for X"
• "计算 X 和 Y 的结合自由能" or "binding free energy"
• "这个蛋白稳定吗" or "protein stability analysis"
• "蛋白-配体相互作用模拟"
• User provides a PDB ID, UniProt ID, or protein structure file

Prerequisites Check

Before starting any simulation, verify the environment:

bash: python3 << 'PYEOF'
import sys

checks = {"openmm": False, "ambertools": False, "mdtraj": False, "pdbfixer": False, "nglview": False}

try:
    import openmm
    checks["openmm"] = True
    print(f"✅ OpenMM {openmm.__version__}")
except ImportError:
    print("❌ OpenMM not installed")
    print("   Install: conda install -c conda-forge openmm")

try:
    import parmed
    checks["ambertools"] = True
    print("✅ AmberTools (via parmed)")
except ImportError:
    print("⚠️  AmberTools not installed (optional, for ligand parameterization)")
    print("   Install: conda install -c conda-forge ambertools")

try:
    import mdtraj
    checks["mdtraj"] = True
    print(f"✅ MDTraj {mdtraj.__version__}")
except ImportError:
    print("❌ MDTraj not installed (needed for analysis)")
    print("   Install: pip install mdtraj")

try:
    import pdbfixer
    checks["pdbfixer"] = True
    print("✅ PDBFixer")
except ImportError:
    print("❌ PDBFixer not installed (needed for structure preparation)")
    print("   Install: conda install -c conda-forge pdbfixer")

if not checks["openmm"]:
    print("\n⛔ Cannot run MD simulations without OpenMM.")
    print("Recommend: conda create -n md python=3.11 openmm pdbfixer mdtraj parmed -c conda-forge")
    sys.exit(1)

print("\n✅ Environment ready for MD simulations")
PYEOF

If OpenMM is not available, report clearly and do not attempt the simulation.

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Pipeline

Step 1: Structure Retrieval