Bug in solvate
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 loop. (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.
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.