GROMACS

Running the gmx solvate program with an existing box works, but the -shell option, supposed to make a spherical droplet around a solute yields zero solvent molecules.

Example:

Version 4.6 gives:
% genbox -cp after_em.gro -cs spc216 -o b4em_sol.gro -shell 1.2
<snip>
Number of SOL molecules: 1123

Version 5.0 gives:
% gmx solvate -cp after_em.gro -cs spc216 -o b4em_sol.gro -shell 1.2
<snip>
Number of SOL molecules: 7039

Version 5.1 gives:
% gmx solvate -cp after_em.gro -cs spc216 -o b4em_sol.gro -shell 1.2
<snip>
Number of SOL molecules: 0