Refernece MD data - Githubissues

torchmd / torchmd-protein-thermodynamics

Tutorials and data necessary to reproduce the results of publication Machine Learning Coarse-Grained Potentials of Protein Thermodynamics

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Refernece MD data #12

Closed MaciejMajew closed 9 months ago

MaciejMajew commented 1 year ago

Reference MD simulations contain only xtc and no reference topology file. I checked trpcage, maybe others have it. @AdriaPerezCulubret can you add generators somewhere?

AdriaPerezCulubret commented 1 year ago

Checked chignolin and villin and they have filtered.psf and filtered.pdb topologies. But it's true that trpcage doesn't. I'll fix it, and I'll try to check the others and see if topologies are missing also.

AdriaPerezCulubret commented 1 year ago

Uploaded trpcage with topologies (filtered.psf and filtered.pdb)

ynshen commented 9 months ago

Hi @AdriaPerezCulubret, thanks for sharing this awesome work! I just downloaded the reference MD data but found several trajectories missing topology files. Could you share these topology files or how to generate them? Thanks!

Here are trajectories missing topology files:

a3D_1/a3D_2
bba
lambda
ntl9
proteing_2 (but proteing_1 has)
wwdomain_1/wwdomain_2

AdriaPerezCulubret commented 9 months ago

I've updated the .tar.gz files for all reference trajectories mentioned, now they include the topology files.

Let me know if I'm missing any.