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ajkluber / model_builder

Represents coarse-grain models for easy simulation and parameter fitting.
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debye huckel #15

Open TensorDuck opened 8 years ago

TensorDuck commented 8 years ago

When I try model_builder to source a parameters folder for the awsem package, I end up getting an error. It looks like it's looking for a debye huckel parameters in a file that doesn't have that heading. Is that a typo, or are there updated parameter files for including debye huckel?

Eitherway, a propose a solution: set this up so that if during the source step, it doesn't find the parameters, it won't try to parameterize them later. I can implement this quickly.

ajkluber commented 8 years ago

The electrostatic interactions that Min-Yeh has added are on the amylometer branch of AWSEM: https://github.com/adavtyan/awsemmd/tree/amylometer

Debye Huckel section is on this line.

ajkluber commented 8 years ago

For AWSEM parameters I think we should have options to source parameters from a file or use hardcoded defaults. Sourcing would only be necessary for parameters that may change, such as the Debye-Huckel screening length.

The AwsemModel class currently doesn't output its own fix_backbone_coeff.dat (I think) but it should. I will double check this.

TensorDuck commented 8 years ago

Ah okay. It looks like the awsem has different files for different interactions. I think the best way to fix this would be to add checks in our python code that if they don't find an interaction section on sourcing, then the code won't attempt to parameterize the Hamiltonian with those interactions.

I can push these changes with my latest additions to the awsem model if you weren't planning on doing more development work.

ajkluber commented 8 years ago

Go ahead and merge when you are ready. I will have to look at this another day.