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fhh2626 / BFEE2

binding free energy estimator 2
GNU General Public License v3.0
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Question: update centers #98

Closed ReneHamburger1993 closed 1 year ago

ReneHamburger1993 commented 1 year ago

Hi, I got a question about the statement: "To calculate the binding free energy:

1.1 run 000_eq/000.1_eq.conf 1.2. (optionally) run 000_eq/000.2_updateCenters.py (If this is done, then there is usually no need to change restraining centers after steps 3.x.)"

I am a litte confused by the word "after". What does "after steps 3.x." actually mean? Do I need to update the centers again with the position of the respective PMF minima when using the 000_eq/000.2_updateCenters.py pyscript or not?

https://github.com/fhh2626/BFEE2/blob/92352ae884d4499f27885d013410852370495f0f/BFEE2/templates_readme/Readme_NAMD_Geometrical.txt

ReneHamburger1993 commented 1 year ago

Point being, I would not need to write some lines of code to automate this and can just pass my generated jobscripts to the cluster in dependence or even run the angle abf runs in parallel as well if no update was necessary.

fhh2626 commented 1 year ago

Point being, I would not need to write some lines of code to automate this and can just pass my generated jobscripts to the cluster in dependence or even run the angle abf runs in parallel as well if no update was necessary.

000.2_updateCenters.py updates the restraining centers using the results of the equilibration. You can then submit jobs one by one without change config files.

ReneHamburger1993 commented 1 year ago

Okay thanks for the clarification! 👍 Suggestion: A little textual update in that readme file above might help others as well :)