| 81 | | If we parse in the config files again, we will not have two separate molecules, addressable by indices 0 and 1, but a single one. This is bad. Let's do a graph analysis of the system |
| | 81 | Now, we have fooled around a bit with the molecular system. We should briefly start from scratch and this may also serve as a test for you, measuring how well you have paid attention so far. I.e. perform the following steps |
| | 82 | 1. delete test.conf |
| | 83 | 2. parse in water.xyz into a now empty test.conf (hence, don't forget to extend ''-o xyz'' to ''-o pcp xyz'' for this step) |
| | 84 | 3. change the box to 25,25,25 |
| | 85 | 4. shift the present molecule by (5,5,5) |
| | 86 | 5. parse in another while shifting it by 15,15,15 at the same time. |
| | 87 | |
| | 88 | If we then parse in the config files again, we will not have two separate molecules, addressable by indices 0 and 1, but a single one. This is bad. Let's do a graph analysis of the system |
