[Apbs-users] APBS-0.4 & sdens parameter

[Gernot K. <ger...@we...>]

Hi there!
Can you give a more detailed description of the use of SDENS and the 
changes you've made to the dielectric accessibility routines (references)?

In the changelog you're claiming that the new related code is 30-50% 
faster. However, to me it APBS-0.4 feels *much* slower and memory 
demanding using mol/smol based surfaces and SDENS=10.0 (and MGMANUAL). 
This slow down seems to be exclusively due to the calculation of 
dielectric accessibility as APBS 0.4 runs almost as fast as 0.3.2 using 
predefined diel/kappa-maps. This is especially problematic as I'm doing 
titration calculations using APBS involving the calculation of the LPBE 
hundreds of times for a protein.

Any comments would be appreciated. TIA!

Greetings,
Gernot