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Bug #2119

gmx solvate -shell does not add anything

Added by David van der Spoel over 2 years ago. Updated almost 2 years ago.

Status:
Closed
Priority:
Normal
Category:
-
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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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

after_em.gro (4.97 KB) after_em.gro David van der Spoel, 02/09/2017 07:07 AM

Associated revisions

Revision 54d906f1 (diff)
Added by David van der Spoel over 2 years ago

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

History

#1 Updated by Gerrit Code Review Bot over 2 years ago

Gerrit received a related patchset '1' for Issue #2119.
Uploader: David van der Spoel ()
Change-Id: gromacs~release-5-1~I61b04457ddcf34b789d590d610c2c365f84a17db
Gerrit URL: https://gerrit.gromacs.org/6461

#2 Updated by Gerrit Code Review Bot over 2 years ago

Gerrit received a related patchset '1' for Issue #2119.
Uploader: David van der Spoel ()
Change-Id: gromacs~release-2016~I88feef55f33c7076b9c27a9831ee04d890333b76
Gerrit URL: https://gerrit.gromacs.org/6468

#3 Updated by David van der Spoel over 2 years ago

  • Status changed from New to Resolved

#4 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Resolved to Closed

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