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galaxyproject / training-material

A collection of Galaxy-related training material
https://training.galaxyproject.org
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MD : NVT equilibration step #3224

Open nagoue opened 2 years ago

nagoue commented 2 years ago

@simonbray Hello, In the tutorial : https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/setting-up-molecular-systems/tutorial.html at NVT equilibration step, I couldn't get temperature convergence to 300K. In the video, at 36:33 min, I got similar values as yours starting with -839375 K but at 36:38 min you are doing the Extract energy components graph and got 293.4 K. I didn't catch what you did between those 2 time points. May you clarify this step ? Cheers,

simonbray commented 2 years ago

Hi @nagoue, I don't think there is anything particular happening between those points, you should do the following:

  1. Visualize the tabular file using the jqplot Line chart visualization
  2. Plot column 1 against column 2
  3. You should see a plot something like https://www.youtube.com/watch?v=LjW3nES04bI&t=2208s (36:48). The exact values are not important but it should fluctuate somewhere around 300 K.

If not, feel free to share a history with me via Gitter.

nagoue commented 2 years ago

Hi @simonbray, not sure to know how to share a history on Gitter... so here it comes But basically, I have similar result as your dataset 41 with high low negative values and can't get what you show on dataset 44 with values converging around 300K. Galaxy-Workflow-GTN_htmd-analysis.zip Thanks