Bug in solvate - Redmine #2523
Archive from user: marc Barbry
Hi,
I found a bug regarding bad formatted input pdb file in the solvate
package.
Using a pdb file (H2o-nocell.pdb) without any cell indication just lets
the program running since it get stuck in a while loo (solvate.cpp, line
~250).
This is because the variable box[i][i] = 0.0, therefore xcg does not
increment.
To reproduce the error, you can run (see attached files)
gmx solvate -cs H2O-nocell.pdb -cp centered.gro -p topol.top -o solvated.gro
The input file should be correctly check in order to avoid such issues.
Best regards,
Marc Barbry
(from redmine: issue id 2523, created on 2018-05-25 by gmxdefault, closed on 2018-06-04)
- Changesets:
- Revision a59917f9 by Paul Bauer on 2018-05-30T07:25:46Z:
Disallow use of empty box information in solvent files
An empty box information in a solvent file presented to gmx solvate
could case an infinte loop because the current coordinate would always
be incremented by zero. Disallowed by introducing new function that
checks for proper box information.
Fixes #2523
Change-Id: I461509f8aafa2048253faf85ccbe388bbbaf80a7
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