Step 4 - Equilibrate the System

We’re now in a position to run our initial equilibration of the system, so let’s set the simulation running.

Simulation ⇨ Run

…or…

Ctrl-R

It’s useful to observe the energy of the configuration as we’re equilibrating our system, since once this reaches a steady value we can begin to think about what to do next. The Energy module provides plots of the various energy components:

Go to the   Evolve (Standard)   tab

Select the Energy module and click the Output button to see the module’s output graphs

You’ll see several curves on the graph, including the total energy (black line) which is the sum of the internal (intramolecular) bond and angle and the intermolecular (i.e. Lennard-Jones plus coulomb) terms. The MD module is set to only run if the total energy of the configuration is stable, but you should be able to notice when it kicks in as the bond (green line), angle (purple line), and total (blue) intramolecular energies which are constant during the Monte Carlo steps will suddenly drop to lower values. There will be some variation of the components up and down, but for a system of 1000 water molecules the total energy should approach a value of around -35×10³ kJ mol^-1 with the intermolecular energy around -44×10³ kJ mol^-1.

The energy will take a few hundred iterations to stabilise, so while we’re waiting we’ll take an initial look at the comparison between simulation and experiment in the next section.

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