matsunagalab
Official@matsunagalab · Japan
Offers specialized computational chemistry modules for molecular dynamics preparation, production simulation, and trajectory analysis on high-performance computing clusters.
Agent Skills by matsunagalab
Showing 5 vetted skills indexed across 1 GitHub repositories.
matsunagalabMD Prepare
Automate molecular dynamics preparation workflows from structure acquisition to topology generation.
matsunagalabMD Production
Run production MD simulations from equilibrated checkpoints via MDClaw CLI.
matsunagalabMD Equilibration
Automate MD equilibration workflows from minimization through NPT steps.
matsunagalabHPC Run
Submit and manage SLURM-based MDClaw workloads on HPC clusters.
matsunagalabMD Analyze
Concatenate molecular dynamics trajectories into a combined DCD and reference PDB.
Frequently Asked Questions About matsunagalab
FAQPage SchemaWhat specific molecular dynamics tasks are supported?▼
The suite supports the full lifecycle of molecular dynamics, including structure acquisition, topology generation, minimization, NPT equilibration, and production simulation. It further enables post-simulation trajectory concatenation into standard DCD and PDB formats for structural analysis.
Which technical personas benefit from these capabilities?▼
Computational chemists, biophysicists, and research engineers managing large-scale molecular simulations on high-performance computing environments will find these modules essential for standardizing simulation pipelines and managing complex job submissions.
What are the infrastructure prerequisites for running these simulations?▼
Execution requires access to a high-performance computing environment utilizing the SLURM workload manager. Users must have the MDClaw environment configured on their cluster to facilitate job submission, checkpoint management, and trajectory processing.