Step 2 - Set up a Configuration
Time to create a suitable liquid configuration for our simulation using the predefined “simple random mix” generator:
Configuration ⇨ Create… ⇨ Simple random mix
Choose the benzene species and press Select
Double-click on the tab title and change its name to
Liquid
In the interests of speed, we’ll use the default number of molecules (100) for the simulation, but we will need to set the correct density. We’ll use chemical units of g/cm3 to specify it:
Open the settings for the
Parametersnode
Check that the value of the “rho” variable is 0.876. Note that this is “just a number” - units are given in the
Addnode when we reference this value
Open the settings for the
Addnode
Make sure that the units for the Density are set to
g/cm3and that it references our parameterrho
Click Regenerate to recreate the configuration with our adjusted parameters
The resulting box will have a side length of just over 24.5 Å.
Initial, randomised benzene box containing 100 molecules
Since the molecules were added to the box completely at random, there will most likely be some that overlap quite a lot. Since our molecule has a ring, this can lead to situations where molecules become interlocked, and which will persist throughout the simulation unless we deal with them. The easiest thing to do is to use what Dissolve (and EPSR) call “size factor scaling”. Basically, this allows the configuration box and the positions of the molecules to be scaled temporarily, removing bad overlaps and letting molecules move safely apart. The factor by which the box is scaled is reduced gradually until a value of 1.0 (i.e. the initial system size) is regained.
In anticipation of some bad contacts:
Liquid configuration tab
Set the Requested value for the Size Factor Scaling to 10.0
Finally, before we move on, we will have to reduce our pair potential range from the default of 15 Å since this is larger than the half the maximum width of our simulation box.
Forcefield tab, Pair Potentials section
Reduce the pair potential Range from 15 to 12 Å
For a cubic box, you can’t have a cutoff value greater than half the box length, as this means that a given atom will ‘see’ other atoms twice because of the periodic boundary conditions.