What types of trajectory analysis can I perform?

You can perform RMSD/RMSF calculations, protein-ligand contact analysis, flexibility mapping, and distance-based structural measurements.

Does it help with system preparation?

Yes, it includes scripts for loading PDB files, adding hydrogens, solvating systems with water models like TIP3P, and adding neutralizing ions.

Is this suitable for drug-ligand binding studies?

Absolutely. It features specific modules for setting up protein-small molecule systems and analyzing interaction interfaces and binding energetics.

Can this skill handle GPU-accelerated simulations?

Yes, the provided OpenMM workflows include configurations for CUDA and OpenCL platforms to leverage GPU acceleration for production-grade MD.

What simulation engines are supported by this skill?

This skill is optimized for OpenMM for running simulations and MDAnalysis for processing trajectories from various packages like GROMACS, AMBER, and CHARMM.

Molecular Dynamics & Structural Biology

Name: Molecular Dynamics & Structural Biology
Author: henriquescastilho

byhenriquescastilho

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데이터 과학 및 ML

Performs and analyzes molecular dynamics simulations using OpenMM and MDAnalysis for biophysics and drug discovery research.

This skill integrates advanced molecular dynamics (MD) workflows into Claude, enabling researchers to set up, run, and analyze complex molecular systems. By leveraging OpenMM for high-performance simulations and MDAnalysis for trajectory processing, it covers the entire pipeline from PDB preparation and force field selection to production MD and statistical analysis. It is designed for applications in protein stability studies, ligand binding characterization, and conformational sampling, providing a robust Python-based framework for structural biology and biophysical modeling.

주요 기능

01Comprehensive trajectory analysis including RMSD, RMSF, and contact mapping

02Energy minimization and multi-stage equilibration (NVT/NPT) protocols

03High-performance simulation setup using OpenMM with GPU support

04Automated system preparation from PDB files including solvation and ionization

05Native support for major force fields including AMBER14 and GAFF2

061 GitHub stars

사용 사례

01Analyzing the impact of genetic mutations on protein structural stability

02Exploring conformational ensembles of intrinsically disordered proteins

03Characterizing binding modes and residence times for drug-ligand complexes

주요 기능

01Comprehensive trajectory analysis including RMSD, RMSF, and contact mapping

02Energy minimization and multi-stage equilibration (NVT/NPT) protocols

03High-performance simulation setup using OpenMM with GPU support

04Automated system preparation from PDB files including solvation and ionization

05Native support for major force fields including AMBER14 and GAFF2

061 GitHub stars

사용 사례

01Analyzing the impact of genetic mutations on protein structural stability

02Exploring conformational ensembles of intrinsically disordered proteins

03Characterizing binding modes and residence times for drug-ligand complexes