Can I run these simulations on a GPU?

Yes, the skill includes configurations to leverage CUDA or OpenCL platforms, allowing you to take advantage of GPU acceleration if available on your system.

What tools does this skill use for simulations?

The skill primarily utilizes OpenMM for running high-performance simulations and MDAnalysis for processing and analyzing the resulting trajectory data.

Does it support ligand binding studies?

Absolutely. It includes specific workflows for setting up protein-ligand systems and performing contact analysis to track interactions over time.

What structural analysis metrics are provided?

The skill includes built-in functions for calculating Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and residue-specific contact maps.

Molecular Dynamics Simulation & Analysis

Name: Molecular Dynamics Simulation & Analysis
Author: Yezez9

byYezez9

0•

Data Science & ML

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

This skill empowers researchers and developers to set up, execute, and analyze complex molecular dynamics simulations directly within their computational workflow. It provides comprehensive support for OpenMM as a high-performance simulation engine and MDAnalysis for processing trajectories, covering everything from system preparation and energy minimization to advanced structural analysis like RMSD, RMSF, and contact mapping. Whether studying protein stability, ligand binding, or conformational changes, this tool automates the intricate boilerplate required for professional-grade biophysics simulations.

Key Features

010 GitHub stars

02Energy minimization and multi-stage NVT/NPT equilibration workflows

03GPU-accelerated simulation support via CUDA and OpenCL integration

04Protein-ligand contact mapping and structural fluctuation tracking

05Automated system preparation with OpenMM force fields and solvation

06High-performance trajectory analysis including RMSD and RMSF calculations

Use Cases

01Evaluating the impact of specific genetic mutations on a protein's structural stability

02Modeling the time-dependent conformational ensembles of intrinsically disordered proteins

03Characterizing the binding affinity and residence time of a drug candidate to a target protein

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent molecular-dynamics

For use in Claude.ai and ChatGPT

Key Features

010 GitHub stars

02Energy minimization and multi-stage NVT/NPT equilibration workflows

03GPU-accelerated simulation support via CUDA and OpenCL integration

04Protein-ligand contact mapping and structural fluctuation tracking

05Automated system preparation with OpenMM force fields and solvation

06High-performance trajectory analysis including RMSD and RMSF calculations

Use Cases

01Evaluating the impact of specific genetic mutations on a protein's structural stability

02Modeling the time-dependent conformational ensembles of intrinsically disordered proteins

03Characterizing the binding affinity and residence time of a drug candidate to a target protein