Step 5 - Calculate Baseline Properties
Now that the analysis processing layer is prepared, we need to run it for a while in order to get some good statistics on our quantities. A good 500 iterations (preferably 1000) is needed to get the statistics for the 2D map, so let’s ask Dissolve to run for a set number of steps:
Simulation ⇨ Run For…
Enter
1000and click
Dissolve will now iterate for 1000 iterations and stop - you can see the estimated time remaining to complete these 1000 steps in the status bar at the bottom of the main window. Now might be a good time to have a drink, or write that email you’ve been putting off. If you think 1000 iterations is going to take too long, press Escape to stop the simulation and go for 500 iterations instead.
To see what’s being calculated, go back to the
AxisAngle module and look at its output section:
Go to the
Analysis layer
Click the
We have three graphs - top-left is the radial distribution function between the centres-of-geometry of the benzene, while the bottom-left is the angle histogram of the z-axis angles (averaged over all distances). The main graph to the right shows the distance-angle map of the two quantities. You might want to explore the latter in 3D space, rather than a top-down view - you can change the view style for the plot in the toolbar at the top (change the view type from XY to 3D).
Once the iterations have completed, we need to do a bit of housekeeping.
Snapshot the Current Data
Let’s save the current data now, as it represents our reference point against which we’ll compare things later on:
File ⇨ Save Restart Point…
Change the filename to
reference.restartand click
You might also find it useful to copy images of the graphs here to help with comparison later on - right-click on an empty part of the graph and select Copy to clipboard - or you can right-click on a particular curve and save the data directly in order to plot it in some other external software.
Clear the Current Data
Since we’re about to refine our simulation against experimental data and re-run the analysis, we don’t want to retain any of the currently-calculated quantities. We can request that Dissolve clear all of the data generated by modules and reset the simulation back to an “empty” state. Critically, the current contents of any configurations will remain untouched (i.e. our equilibrated box will remain in its present state, so we can proceed directly on with the simulation). It will also reset the iteration counter to zero.
Time to get rid of that data…
Simulation ⇨ Clear Module Data
Accept the consequences, and click
Turn off the Analysis Layer
We need to refine the simulation before we calculate our properties again, so we need to temporarily turn off our analysis layer:
Go to the
Disable the layer by clicking the Layer Enabled? button at the top-left of the tab so it displays