GROMACS molecular dynamics skill for nanoparticle-biomolecule interaction simulations
The GROMACS MD Executor skill provides molecular dynamics simulation capabilities specialized for nanoparticle-biomolecule interactions, enabling investigation of drug delivery systems, protein-surface interactions, and membrane penetration.
System Preparation
Equilibration
Production and Analysis
{
"nanoparticle_file": "string",
"biomolecule_file": "string",
"force_field": "CHARMM36|AMBER|Martini",
"simulation_type": "binding|membrane|protein_corona",
"temperature": "number (K)",
"simulation_time": "number (ns)"
}
{
"binding_energy": "number (kJ/mol)",
"contact_residues": ["string"],
"rmsd": "number (nm)",
"interaction_analysis": {
"hydrogen_bonds": "number",
"hydrophobic_contacts": "number"
},
"trajectory_file": "string"
}