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Software for biomolecular electrostatics and solvation calculations
http://www.poissonboltzmann.org/
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Units in geometric flow examples #6

Open sobolevnrm opened 7 years ago

sobolevnrm commented 7 years ago

Are the units in the geometric flow examples really kcal/mol/A^n? They should be kJ/mol/A^n.

keith923 commented 7 years ago

Those files hail back to at least Andrew, and possibly from the Fortran code/paper (with Dennis, et. al.). I'll have to dig in to verify the latter.

keith923 commented 7 years ago

I'm not trying to assert that the example is correct. Only that the value there appears to have come from Parameterization of a geometric flow implicit solvation model.

The Calculation procedure section states:

For each force-field and solute dielectric coefficient value, we calculated the root mean square error (χ) between the experimental (ΔGexpt) and calculated (ΔGcalc) solvation free energies for the entire 17 molecule set in the pressure-surface tension (p-γ) parameter space. A grid-based parameter optimization was performed over a range that generally included p values from 10−4 to approximately 0.1 kcal/(mol·Å3) and γ values from 10−5 to approximately 0.1 kcal/(mol·Å2). The exact ranges of values and search increments used to explore the p-γ parameter space for each force-field are summarized in Supporting Information Table S1 for ϵs = 1. We denote the minimum value of χ in the p-γ parameter space as χmin. Therefore, the (p,γ) point at which χ = χmin, corresponds to the optimal values of pressure, popt, and surface tension, γopt.

sobolevnrm commented 7 years ago

Same values as the paper as well? Regardless, we should switch to kJ for consistency with the rest of APBS.

On Mon, Jun 26, 2017 at 4:12 PM, Keith T. Star notifications@github.com wrote:

I'm not trying to assert that the example is correct. Only that the value there appears to have come from Parameterization of a geometric flow implicit solvation model.

The Calculation procedure section states:

For each force-field and solute dielectric coefficient value, we calculated the root mean square error (χ) between the experimental (ΔGexpt) and calculated (ΔGcalc) solvation free energies for the entire 17 molecule set in the pressure-surface tension (p-γ) parameter space. A grid-based parameter optimization was performed over a range that generally included p values from 10−4 to approximately 0.1 kcal/(mol·Å3) and γ values from 10−5 to approximately 0.1 kcal/(mol·Å2). The exact ranges of values and search increments used to explore the p-γ parameter space for each force-field are summarized in Supporting Information Table S1 for ϵs = 1. We denote the minimum value of χ in the p-γ parameter space as χmin. Therefore, the (p,γ) point at which χ = χmin, corresponds to the optimal values of pressure, popt, and surface tension, γopt.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Electrostatics/apbs-pdb2pqr/issues/479#issuecomment-311207391, or mute the thread https://github.com/notifications/unsubscribe-auth/AB1_2F38HZOlt0gXFY0qJMfVpDS8Mh8Tks5sIDrigaJpZM4OF8hM .

sobolevnrm commented 4 years ago

@mvaliev -- another geometric flow issue; would you take this?