Step Two: Define the Unit Cell
Defining the unit cell for a pulling simulation is not unlike defining the unit cell for any other simulation. There is, however, one major consideration. One must allow enough space in the pulling direction to allow for a continuous pull without interacting with the periodic images of the system. That is, the minimum image convention must be continually satisfied, and as well, the pull distance must always be less than one-half the length of the box vector along which the pulling is being conducted. Why, you may ask?
GROMACS calculates distances while simultaneously taking periodicity into account. This, if you have a 10-nm box, and you pull over a distance greater than 5.0 nm, the periodic distance becomes the reference distance for the pulling, and this distance is actually less than 5.0 nm! This fact will significantly affect results, since the distance you think you are pulling is not what is actually calculated.
We will be pulling a total distance of 5.0 nm in a 12.0-nm box, to avoid the complications described above. The center of mass of the protofibril will be placed at (3.280, 2.181, 2.4775) in a box of dimensions 6.560 x 4.362 x 12. Use editconf to place the protofibril at this location:
editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12
You can visualize the location of the protofibril within the box using, for example, VMD. Load the structure in VMD and open the Tk console. Type the following (note that > indicates the Tk prompt, not something you actually type):
> package require pbctools > pbc box
You should see something like the following in the VMD window:
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