Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Example YAML files for alternate solvent systems

See original GitHub issue

Are there a collection of yaml file syntax/orders that are available for non-pme solvent systems? I’m still having issues getting pme to work, and would like to use rf in the mean time, but am getting a myriad of lambda_restraints errors that I don’t quite understand.

Issue Analytics

State:
Created 7 years ago
Comments:8 (5 by maintainers)

Top GitHub Comments

1reaction

spadaveccommented, Mar 2, 2017

well now I’m thoroughly spooked; re-running this on a different machine seems to run both rf and pme fine. I’ll investigate this more and get back to you asap. Sorry for the hassle

0reactions

andrrizzicommented, Mar 2, 2017

That’s very weird! The leap script is not aware of what method is used. Can you share the input files? I could try to replicate and see what is the cause of the issue.

Top Results From Across the Web

Systems Header for YAML Files — YANK 0.23.7 documentation

The systems header is where we combine molecules and solvents together ... In the examples, these user defined names are marked as {UserDefinedSystem}...

blues/BLUES_tutorial.ipynb at master - GitHub

An example YAML configuration file can be found in rotmove_cuda.yaml . ... provide an example for generating a system in a cubic box...

Prediction of Solvatochromic Polarity Parameters for Aqueous ...

Solvent polarity is important data being used in solvent selections for preliminary engineering design of chemical processes. In this work, a predictive ...

Chromatography: Solvent Systems For Flash Column

Hydrocarbons: pentane, petroleum ether, hexanes; Ether and dichloromethane: (very similar polarity); Ethyl acetate. The most common two-component solvent ...

Templating YAML in Kubernetes with real code - Learnk8s

While the example shows a useful strategy to compose complex YAML from basic files, it also shows some of the limitations of yq...