molecular-dynamics
Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis
by k-dense-aiFree
Description
molecular-dynamics is an agent skill for running and analysing molecular dynamics simulations with two tools: OpenMM and MDAnalysis. Molecular dynamics models how molecular systems change over time by integrating Newton's equations of motion. OpenMM is a high-performance simulation engine with GPU support, a Python API and flexible force-field support. MDAnalysis reads, writes and analyses trajectories from all the major simulation packages. The skill covers setting up protein and small-molecule systems, defining force fields, and running energy minimisation and dynamics. It then helps with analysis of the resulting trajectories. The reviewed versions are OpenMM 8.6.1 and MDAnalysis 2.10.0. The reference-platform smoke checks used small synthetic systems, and the skill says they do not establish GPU performance or scientific convergence. OpenMM's latest API pages describe a development build, so the installed 8.6.1 API is the reference for the examples. Use it when you need to set up or analyse a simulation of a protein or a drug-like molecule. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars.…
Highlights
- Sets up protein and small-molecule systems
- Force fields and energy minimisation
- OpenMM simulation with GPU support
- MDAnalysis trajectory analysis
- Reviewed on OpenMM 8.6.1 and MDAnalysis 2.10.0
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What tools does it use?
OpenMM for running simulations and MDAnalysis for reading and analysing trajectories.
What does it set up?
Protein and small-molecule systems, force fields, and energy minimisation and dynamics.
Which versions were reviewed?
OpenMM 8.6.1 and MDAnalysis 2.10.0.
Does the review show the results are converged?
No. The smoke checks used small synthetic systems, and the skill says they do not establish GPU performance or scientific convergence.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill molecular-dynamics.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best molecular-dynamics alternatives?
Popular alternatives to molecular-dynamics include marketing-council, cirq and fluidsim. See all molecular-dynamics alternatives