SimTk/openmm — pull request #308 by swails (2014-01-28 18:29:43+00:00)
Title: Improve usability of salt concentration in Amber custom GB forces

OK, this pull request completes (I hope!) the plans laid out in issue #249 (now closed). Users can now specify either implicitSolventKappa or implicitSolventSaltConc in the createSystem function call (with units of 1/length or concentration, respectively). implicitSolventKappa takes precedence if both are specified.

The conversion of implicitSolventSaltConc to implicitSolventKappa is now a function of the system temperature and the solvent dielectric constants. It is based on the same model that the Amber conversion comes from and yields the same mapping of ionic strength -> kappa that Amber does for the same dielectric (78.5) and temperature (298.15).