Allow pdb2gmx to handle cyclic molecules

Allow pdb2gmx to handle cyclic molecules

This has been a long outstanding issue with the code not being able to
do this.

Cyclic molecules are detected by checking if chain ends are within bonding
distance from each other. This does not detect cyclic molecules over PBC
boundaries.

Initial patch proposed by Boris Timofeev.

Resolves #3571

Change-Id: Ic25e46a12fef5fb46748dc0497f469b5834d4886