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DeepDriveMD / DeepDriveMD-pipeline

DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations
MIT License
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Where are the initial pdb files? #55

Closed EmperorJia closed 2 years ago

EmperorJia commented 2 years ago

Hello! I'm replicating this project and I've got a question. In DeepDriveMD-pipeline/test/bba/lassen-integration.yaml, I see initial_pdb_dir: /p/gpfs1/brace3/data/bba/ddmd_input, but I didn't find this directory in the project, except for DeepDriveMD-pipeline/data/bba/system. Are they the same? If not, would you please provide me the initial pbd files? Thanks in advance.

braceal commented 2 years ago

Thanks for your interest! The initial_pdb_dir config option allows you to input any molecular system. The data in DeepDriveMD-pipeline/data/bba/system is an example of how a single structure could be input to initialize DeepDriveMD.

Here is a note about it in our readme: https://github.com/DeepDriveMD/DeepDriveMD-pipeline#note-on-input-data

The /p/gpfs1/brace3/data/bba/ddmd_input is a specific path used in one of our tests, to work with your own data, update this path in the config to be an absolute path to your system directory (as shown in the note).

EmperorJia commented 2 years ago

Oh, I got it. Thanks for your quik reply!