jvita
commented
11 months ago Some notes for improving the upload template:
- The template should enable selecting molecule type, instead of only elements. I'm sure there's a tool out there somewhere from generating element lists from molecule names.
- CS construction should support pre-built groups better. For example, the data here is grouped as
/ ; these should be automatically converted to CSs somehow. I didn't add CS definitions here because I didn't want to have to add 100 lines of regexes, one for each group.
gpwolfe
Name
Josh Vita
Email
vita1@llnl.gov
Dataset name
AIMD-Chig
Authors
Tong Wang, Xinheng He, Mingyu Li, Bin Shao, Tie-Yan Liu
Links
Dataset description
This dataset covers the conformational space of Chignolin with DFT-level precision. We sequentially applied replica exchange molecular dynamics (REMD), conventional MD, and ab initio MD (AIMD) simulations on a 10 amino acid protein, Chignolin, and finally collected unparalleled 2 million biomolecule structures with quantum level energy and force records.
File details
Data repo includes README specifying folder contents/structure, which reports that the data is stored in XYZ format and is grouped by "anchor".
In total, looks to be ~15GB (zipped).
Method
DFT
Method (other)
No response
Software
ORCA
Software (other)
No response
Software version(s)
4.2.1
Additional details
M06-2X functional in conjunction with 6–31 G* basis set was employed for the calculation
Property types
Atomic forces, Potential energy
Other/additional property
No response
Property details
Elements
Chignolin
Number of Configurations
2,000,000
Naming convention
Names can likely be generated by//snapshot.xyz.
Configuration sets
No response
Configuration labels
No response
Distribution license
CC BY 4.0
Permissions