Does it support GPU acceleration?

Absolutely. The skill includes specific parameters for CUDA platform selection and device indexing to maximize simulation throughput using OpenMM.

Can this skill handle simulation restarts?

Yes, it supports robust checkpointing and can automatically restart simulations from the last saved state, appending trajectory data to existing DCD files.

What is Hydrogen Mass Repartitioning (HMR)?

HMR is a performance optimization that redistributes mass from heavy atoms to hydrogens, allowing the use of a 4 fs timestep to significantly increase simulation speed.

Is this skill compatible with HPC environments like SLURM?

Yes, it includes tools for managing module loads, environment variables, and simulation timeouts specifically tailored for high-performance computing clusters.

Molecular Dynamics Simulation Runner

Name: Molecular Dynamics Simulation Runner
Author: matsunagalab

bymatsunagalab

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数据科学与机器学习

Executes production-grade molecular dynamics simulations using MDClaw and OpenMM with automated equilibration and HPC support.

This skill enables Claude to manage the entire lifecycle of a production molecular dynamics simulation, bridging the gap between initial preparation and final data collection. It automates complex simulation protocols including energy minimization, multi-stage equilibration (NVT/NPT), and long-term production runs. Designed for computational biophysicists, it provides specialized support for GPU acceleration via CUDA, Hydrogen Mass Repartitioning (HMR) for performance optimization, and robust checkpoint/restart logic for high-performance computing (HPC) environments like SLURM, ensuring simulations are both efficient and resilient to job timeouts.

主要功能

011 GitHub stars

02Automated multi-stage equilibration protocols including NVT heating and NPT production.

03Specialized handling for membrane-embedded systems using semi-isotropic pressure coupling.

04Robust checkpointing and restart capabilities for long-running HPC and SLURM jobs.

05High-performance GPU acceleration support using the OpenMM CUDA platform.

06Advanced simulation performance optimization via Hydrogen Mass Repartitioning (HMR).

使用场景

01Running 50-500 ns production simulations for protein conformational sampling.

02Executing long-duration simulations on HPC clusters with automated restart logic for SLURM timeouts.

03Setting up staged equilibration protocols for complex membrane-protein systems.

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add matsunagalab/mdclaw md-run

For use in Claude.ai and ChatGPT

Download Skill