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molecular-dynamics

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About molecular-dynamics

M

molecular-dynamics

Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis

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.

View molecular-dynamicsAll AI Skills apps
Price
Free
Made by
k-dense-ai
Category
AI Skills
Website
github.com/k-dense-ai/scientific-agent-skills/molecular-dynamics