torchmd-protein-thermodynamics
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torchmd
Tutorials and data necessary to reproduce the results of publication Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
Hi, just doublechecking - what are the units of k0, req, phi_k, epsilon and sigma in prior_force_field.yaml?
Hello, Thank you for the awesome work provided. Upon reading both the paper and the tutorial, I noticed that the tutorial focuses exclusively on a single protein. During the process...
We have been trying to run '3-Tutorial-CG-Simulation-analysis.ipynb', which requires htmd, but an htmd version does not seem to be provided in environment files in the repo. The current version of...
Hello, What is the version of torchmd-net used in this work? It seems that loading the model shared in the repo is compatible with older version of torchmd-net.
Hello, I start to use coordinates and delta-forces to train the network. However, when I typed the command "CUDA_VISIBLE_DEVICES=0 python /users/ssyjb1/torchmd-net/torchmdnet/scripts/train.py --conf train.yaml --log-dir train_light" it shows the error below....
Hello, I start the simulating by activating torchmd_protein_thermodynamics. When testing the simulation (python /home/zz/torchmd-master/torchmd/run.py --conf simulate.yaml), it throws an error: ModuleNotFoundError: No module named 'torchmdnet'. Then I activated torchmd-net, however,...
Hello, I am trying to run CLN tutorial model using the following command: `python /torchmd_mamba_env/lib/python3.10/site-packages/torchmd/run.py --conf simulate.yaml` But I see the following error, which shows there is no aggregator argument...
