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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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Model missing aggregator #25

Open mrjoness opened 2 weeks ago

mrjoness commented 2 weeks ago

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 associated with the model (I'm using ../Models/cln/model.ckpt)

model.py 228 load_model
model = create_model(args)

model.py 76 create_model
aggr=args["aggr"],

KeyError:
aggr

I tried manually setting the aggr to "add", "mean", and "max", which fixes this issue and starts a simulation, but in each case I see the following issue:

run.py 265 dynamics
Ekin, Epot, T = integrator.step(niter=args.output_period)

integrator.py 68 step
pot = self.forces.compute(s.pos, s.box, s.forces)

forces.py 84 compute
raise RuntimeError("Found NaN coordinates.")

RuntimeError:
Found NaN coordinates.

Is there some version issue with TorchMD? or is there something else I am doing wrong here?

Thank you

AdriaPerezCulubret commented 5 days ago

Could you tell me which version of torchmd and torchmdnet you have?

mrjoness commented 5 days ago

Hello, yes here are the versions. I followed the mamba installation in the torchmd repo as I was having trouble with the installation instructions here.

torchmd 1.0.2 pypi_0 pypi torchmd-net 2.2.0 cpu_py310h6472234_2 conda-forge