Step 5 - Set up Potential Refinement
Add the standard EPSR refinement layer to your simulation:
Layer ⇨ Create… ⇨ Refinement… ⇨ Standard EPSR
Double-click the EPSR module to open it up as a tab - it’s always useful to see the various overview graphs it provides. We’ll need to set a relatively high starting value for EReq as we are basically dealing with point charges in a box, and so whatever empirical potential is necessary to drive the structure of the system needs to grow large enough to have some effect against the strong Coulombic forces present.
EPSR module tab
Open the Calculation settings group
Set EReq to 50.0
On the R-Factor tab of the EPSR module you will see that the magnitude of the potential (top graph) increases rather quickly to 50 (within 100 steps in the plot below), but the quality of fit as measure by the r-factor (bottom graph) takes rather longer to reach a steady state.
Evolution of empirical potential magnitude (max = 50.0)
Evolution of r-factor (EReq max = 50.0)
The structure factor of the system at this point looks something like this:
Stable structure factor at EReq = 50.0
The question is, can it be better? The answer is, of course, yes - the intensity of the first strong peak in the F(Q) at 1.47 Å is a little low. The empirical potential will eventually sort this out (perhaps with an increase of EReq to 75 or so) but it takes time to get it exactly right.
What does the peak at Q = 1.47 Å correspond to, and why might it be difficult to reproduce?
For the purposes of the example, let’s move on and calculate something from the (semi-) refined structure.