You should use the same surface definition (surface type and probe radius) for all steps of the calculation. However, if the internal and external dielectric values are equal in some parts of the calculation, then the surface won’t actually be calculated for those parts of the calculation.
Pacific Northwest National Laboratory
From: firstname.lastname@example.org [mailto:email@example.com] On Behalf Of Jesper Soerensen
Sent: Wednesday, May 23, 2012 1:48 PM
Subject: [apbs-users] Manual calculation
I am running a manual (mg-manual) calculation with the SE surface.
3 calculations are solvated and 3 are dry like shown in the APBS examples and according to the thermodynamic cycle.
My question is, in the dry set of calculations, should the 'srad' still be 1.4 like in the solvated calculations?
I mean because in the absence of solvent does it make sense to define the SE surface? But at the same time changing it, results in two different surfaces being used and therefore some terms may not cancel out?
I hope you can provide some insight.