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
Double-click on the configuration tab’s 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:
Select the Parameters node in the generator
Set the value of the "rho" variable to
0.876. Note that this is "just a number" - units are given in the Add node when we reference this value
Select the Add node in the generator
The Density keyword will already reference the parameter “rho”, but the units will need to be changed to
g/cm3
Click 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. Benzene has a ring which makes it possible for molecules to become permanently “interlocked”, but we can do our best to remove such contacts by using what Dissolve (and EPSR) call “size factor scaling”. Basically, this allows the configuration box and the positions of the molecules to be scaled (but keeping the internal geometry intact), removing bad overlaps and letting molecules move safely apart. The factor by which the box is scaled is reduced gradually until the initial requested system size is regained (i.e. corresponding to a size factor of 1.0).
In anticipation of some bad contacts:
Go to the 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.
Go to the Forcefield tab, Atom Types / Pair Potentials section
Reduce the pair potential Range from
15to12Å
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.