Liquid.pdb: Sizes detected: {3, 6} and the PBC

[bieniekmateusz]

I've generated a simple box with waters which creates this error:
Possible issue because molecules are not all the same size! Sizes detected: {3, 6}
It seems that the molecule representation merged some molecules together, and in the case I checked, these molecules were across the PBC box.

For example, in my case, these were:
615 = {dict: 3} {'n': 'O', 'e': 'O', 'x': array([ 2.045, -6.207, -9.691])} 616 = {dict: 3} {'n': 'H1', 'e': 'H', 'x': array([ 1.453, -5.484, -9.898])} 617 = {dict: 3} {'n': 'H2', 'e': 'H', 'x': array([ 2.72 , -6.166, -10.369])} 75 = {dict: 3} {'n': 'O', 'e': 'O', 'x': array([ 1.946, -5.065, 8.431])} 76 = {dict: 3} {'n': 'H1', 'e': 'H', 'x': array([ 2.815, -4.679, 8.324])} 77 = {dict: 3} {'n': 'H2', 'e': 'H', 'x': array([ 1.77 , -5.004, 9.37 ])}

However, increasing the size of the PBC box by 0.5 A removed the issue with 6-atom molecules.

I uploaded the liquid.pdb with the corrected PBC. liquid.pdb.txt

I've run a few simulations initially ignoring the comment. Would you expect it to have any substantial impact on the results?

Thanks,
@jthorton