Questions about concentration calibration.

[bowensha-tudelft]

Hi, I find a "*1000" in the last formula of paprika tutorial 1.

Could you please explain the "*1000" here? Because I find in the original paper, it is said that concentration is already adjusted to 1 M so that we can compare simulation values to experimental ones. What is the unit of "280" here? Should it be M^-1 or anything else? If so, why should we "*1000"?

Thanks in advance for your clarification!

Best regards,
Bowen

[jset231]

Hi @bowensha-tudelft, I believe the experimental value is reported in micro Molar (uM), so it becomes 280 x 10^-3 M. But this is the Ka (association), and the Gibbs free energy equation is dG = -RT ln (Kd) = -RT ln (1/Ka). Then Kd = 1/(280 x 10^-3 M) = 280 x 10^3 M.

The reference to 1 M in the paper includes this in the APR calculation when we estimate the work of releasing the restraints in bulk water. Check out Equation (9) in the 2015 paper. The 1 M is the C^0 symbol, which is ~1661 in units of Angstrom^3.