Wat2ions is complementary to DelPhi, the renowned solver of the Poisson-Boltzmann equation. The electrostatic potential map, pre-computed by DelPhi, is used to replace a certain number of water molecules of the bath, surrounding a solvated macromolecule, with ions. The potential on the oxygens of the water molecules is estimated using a 3D cubic spline interpolation of the pre-computed potential. The waters with the largest potential are replaced with chlorides, and the waters with the smallest potential, with sodii. No two ions are placed closer than a certain distance to each other. To avoid placing ions too close to the macromolecule, the potential map should be pre-computed taking into account the ion-free Stern layer around the macromolecule (see DelPhi manual for further details). The coordinates of the macromolecule, the water bath (except the replaced waters), and the placed ions are output to a new PDB file.


If you have questions please send email to the author Alexander Balaeff, at



Same terms as NAMD license


Please see the wat2ions.c source code header for usage information and platform-specific comments.