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Habilidade de dinâmica molecular GROMACS especializada em sistemas biomoleculares, simulações de proteínas e cálculos de energia livre.
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Ler descrição completa Recolher descrição GROMACS Biosim Runner Skill
Purpose
Provide specialized integration with GROMACS for biomolecular simulations including protein dynamics, free energy calculations, and enhanced sampling methods.
Capabilities
Topology preparation and solvation Energy minimization workflows NPT/NVT equilibration protocols Free energy perturbation setup Trajectory analysis (RMSD, RMSF, RDF) Enhanced sampling methods (metadynamics, replica exchange) Usage Guidelines
Use appropriate water models (TIP3P, TIP4P, SPC/E) Select force fields compatible with target biomolecules (AMBER, CHARMM, OPLS) Follow standard equilibration protocols Monitor system stability during production runs Dependencies
GROMACS pdb2gmx MDAnalysis PLUMED (for enhanced sampling) Process Integration
Molecular Dynamics Simulation Setup High-Performance Computing Workflow
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