Fig. 1 | Scientific Data

Fig. 1

From: AIMD-Chig: Exploring the conformational space of a 166-atom protein Chignolin with ab initio molecular dynamics

Fig. 1The alternative text for this image may have been generated using AI.

The overall pipeline to build the AIMD-Chig dataset. The simulations started from the crystal structure of Chignolin (PDB ID: 5AWL). We first explored the conformation sampling via REMD on 8 different temperatures. Then, conventional MD simulations from 100 representative structures derived from REMD were conducted. After such simulations, we projected the raw coordinate space into a 6-D space according to the tIC analysis. On the projected space, we extracted 10,000 cluster centers as the initial structures for ab initio MD simulations and ran 225 steps of ab initio MD with M062X/6-31 G* setting for each. The last 200 steps of each ab initio MD simulation were reported in the dataset.

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