Setting Up and Running a Sophia Simulation

1. Launch Chimera.

2. Within Chimera, click File, then Open...

3. Navigate to the directory where you installed Sophia and double-click on launch_sophia.py.

            (If you don't see that file, click on the File type bar and select "Python".)

4. The Sophia icon should appear in the tool bar on the left side of the main Chimera window.

           Click it. This will launch Sophia and open the Sophia Main window.

5.  In the Sophia Main window, click New Simulation. This should open the Sophia Universe window.

6.  In the Universe window, you must:

            •  load a PDB File

            •  choose a Force Field

            •  load a FF Mod File (optional)

            •  choose a box length

            •  choose a non-bond cutoff distance

7.  Click "Load Universe".

           You should see the atoms and/or bonds in the Chimera window.

           (If you don't, do the next step, and they should appear.)

8.  In the Chimera menu:
            •  select Select / Select All

            •  select Actions / Atoms/Bonds / ball and stick

            •  under the Actions menu, choose a suitable representation

9.  In the Sophia Recipe window, you must:

            •  load a Recipe 

            •  click on one of the ingredients in the recipe    This is essential.

                    (the ingredient must be highlighted in blue, as shown here)

                    (sometimes there is only one ingredient)

            •  optional:  You can edit the highlighted ingredient at this point. 

            •  click "Run Next Ingredient" or "Run All Ingredients".

10.  The simulation will run. When it is complete, the resulting trajectory will be loaded for viewing. This usually happens very rapidly, but it may take a little time, depending on the size of the system and the length of the simulation.