Uses correct conversion from kcal/mol -> kj/mol #825
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timemachine/fe/utils.py
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| @@ -65,7 +67,7 @@ def convert_uM_to_kJ_per_mole(amount_in_uM): | |||
| Binding potency in kJ/mol. | |||
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| """ | |||
| return 0.593 * np.log(amount_in_uM * 1e-6) * 4.18 | |||
| return 0.593 * np.log(amount_in_uM * 1e-6) * constants.KCAL_TO_KJ | |||
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Based on prior notes, I think 0.593 is intended to be molar gas constant * temperature, in units of kcal/mol, but
(1) the temperature may be inconsistent with DEFAULT_TEMP = 300 kelvin
(2) there may be precision loss.
https://www.wolframalpha.com/input?i=molar+gas+constant+*+300+kelvin = 0.5962 kcal/mol
https://www.wolframalpha.com/input?i=molar+gas+constant+*+298+kelvin = 0.5922 kcal/mol
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RT is from the table
https://en.wikipedia.org/wiki/KT_(energy) (measured in kcal/mol)
Note that the T here should probably be consistent with experimental temperatures, not simulation temperatures, if converting labelled data.
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Should we parameterize this to take in an experimental temperature?
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probably but lets default it to the IUPAC convention of 298.15 Kelvin
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We don't have to change this now, but should project-wide DEFAULT_TEMP also be changed from 300 to 298.15?
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(Irrelevant to current PR -- moved to Issue #827 for later reminder)
* Sets default temperature to 298, which is the same as what it was before * Makes one method call the other, to avoid duplication
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