Molecular-Dynamics-Molecular-Cages

AIMD data analysis methods and part of the raw data for the paper "Supramolecular Proton Conductors Self-Assembled by Organic Cages".

View contents on website: Molecular-Dynamics-Molecular-Cages

Methods

The analysis methods are described in the md_ana.ipynb file. You can also view the contents on web page: Detailed methods.

Results

The analysis results are available in the cage1 and cage2 folders. The files in the above folders are:

sys-pos-1.xyz the AIMD raw trajectory file dumped by CP2K code run on Archer2.
cage*_500K.xyz the trajectory file calibrated by fix the centre of mass of the system.
water_com_cage*.xlsx the centre of masses of water molecules
MSD_D_H2O_cage*.xlsx the mean square displacements and diffusion coefficients of water molecules.
hbonds_mic.json the hydrogen bond analysis results, including the number of H-bonds in each frame, the donor, acceptor, the donor-acceptor separation, the D-H···A angle. For cage-2, only 3000 frames are included due to file size limit.
Figures:
- cage*_500K_ave.jpg Average MSD and diffusion coefficient with error bounds.
- cage*_nhbonds_500K.jpg Number of Hydrogen bonds per unique hydrogen bonding donor-acceptor pairs with respect to time.
- cage*_hbond_lifetime_500K.jpg Hydrogen bond lifetime.

Raw data

The raw .xyz trajectory files were dumped for every 5 fs (every 10 AIMD steps), and are large (several hundreds of MB). Part of the raw trajectory data (650 frames obtained by evenly extracting one frame per every 15 frames from the raw data, the time interval between two consecutive frames is 75 fs) have been uploaded to the cage1 and cage2 folders. For our analysis, all frames (over 11,000 frames, > 55,000 fs or 55 ps) in the large raw trajectory files were used. The raw trajectory files can be provided in reasonable request to reproduce our results.

Citation

Our paper was published on JACS Au: Zhenyu Yang, Ningjin Zhang, Lei Lei, Chunyang Yu, Junjie Ding, Pan Li, Jiaolong Chen, Ming Li, Sanliang Ling, Xiaodong Zhuang, and Shaodong Zhang, JACS Au 2022 2 (4), 819-826. Please ensure you cite our paper if you used our methods in your research.

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