Molecular Dynamics simulation of argon liquid and gas

Setting up an input file

for free energy perturbation

Method: create an ion solvated by a box of water molecules from the water_box.psv file provided by INSIGHT. The water box has already been introduced in the second module on the modeling of liquid water. In this module you will create a single atom, say Mg²⁺, and then "soak" it in water to create a solvent box surrounding the ion solute.

Go to the Builder pull-down menu. Use the Fragment/Get command and select hydroxy from the FRAGMENT_WINDOW to create the water molecule. The FRAGMENT_WINDOW will contain a number of groups. These groups can be used individually or can be bonded together. Once a water molecule has appeared on the screen the menu will be altered to allow you select a second fragment. For this module just select Cancel to exit the Fragment pull-down menu. Now you should see a single water molecule in the center of the monitor. Next we need to convert this molecule into a divalent ion.

Still in the Builder go to the Atom/Delete command. When the menu appears, just click on the hydrogens and they will be deleted. When both hydrogens have been deleted you should see a single cross in the middle of the screen. Select Cancel once you have deleted both hydrogens. Then use the Atom/Replace command to change the oxygen into magnesium. A periodic table will appear. Select Mg on the table and that should appear as the Element Type on the menu. Then click on the oxygen and it should turn into magnesium. On my monitor it turns from red to purple and there is an Mg label showing that the atom has been transformed.

Once you have performed this modern alchemy, you solvate this ion in exactly the same way that you solvated the water molecule in the water box module.

Use the Assembly/Cell command on the INSIGHT (upper) menu bar to create a solvent box. The menu choices you should select are

Lengths

a 18.62

b 18.62

c 18.62

Angles

a 90.00

b 90.00

c 90.00

Click on the Center_in_cell box (it should turn yellow). When you select Execute the water molecule will move up and you will see the outline of the solvent box you have created. Select Cancel and the active menu will disappear. Do not be perturbed if the Mg ion has been moved off the screen. I recommend that you not touch the solvent box until after you have completed the Soak step below.

Then select Assembly/Soak

Method: Select PBC for Periodic Boundary Conditions.

Once selected the diamond should turn yellow indicating the selection. You will note that the Solvent File is $INSIGHT_DATA/water_box.psv.

Select Execute.

You will see blue water molecules fill the solvent box.

Once the ion is solvated you can click on Cancel to eliminate the menu.