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 *(from redmine: issue id 2119, created on 2017-02-09 by dspoel, closed on 2017-12-11)* * Changesets: * Revision 54d906f155299a4b1ceeafaa6ceca1a022beb913 by David van der Spoel on 2017-02-27T19:24:32Z: ``` Fixes bug in gmx solvate with -shell that yielded 0 SOL. In the transition from genbox to the new solvate.cpp some incorrect logic was introduced. Added test for -shell. Implemented test for conf files that check the title and number of atoms. In principle this could be extended to other structure files. Fixes #2119 Change-Id: I88feef55f33c7076b9c27a9831ee04d890333b76 ``` * Uploads: * [after_em.gro](/uploads/e24c3e6fb70475bf75ce1f7a6f25de0a/after_em.gro)