Bug #2119
gmx solvate -shell does not add anything
Description
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
Associated revisions
History
#1 Updated by Gerrit Code Review Bot about 4 years ago
Gerrit received a related patchset '1' for Issue #2119.
Uploader: David van der Spoel (davidvanderspoel@gmail.com)
Change-Id: gromacs~release-5-1~I61b04457ddcf34b789d590d610c2c365f84a17db
Gerrit URL: https://gerrit.gromacs.org/6461
#2 Updated by Gerrit Code Review Bot about 4 years ago
Gerrit received a related patchset '1' for Issue #2119.
Uploader: David van der Spoel (davidvanderspoel@gmail.com)
Change-Id: gromacs~release-2016~I88feef55f33c7076b9c27a9831ee04d890333b76
Gerrit URL: https://gerrit.gromacs.org/6468
#3 Updated by David van der Spoel about 4 years ago
- Status changed from New to Resolved
Applied in changeset 54d906f155299a4b1ceeafaa6ceca1a022beb913.
#4 Updated by Erik Lindahl about 3 years ago
- Status changed from Resolved to Closed
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