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# A Typical Simulation Session Let us consider a typical session of molecular dynamics simulation taking as an example simulation of acetonitrile–water mixture. We begin with building a box with a mixture of acetonitrile and water, then prepare it for molecular dynamics simulation, start the simulation and will observe some results. This typical example demonstrates most of the program features. Here we list all user manipulations without detailed explanations. The main operation techniques are explained in detail in the subsequent sections. We will use already prepared files describing models of acetonitrile and water. Open the MeCN.hin file (File > Open menu). The model window with acetonitrile molecule appears. Add water molecule (File > Add menu). The lower panel appears: Press the up arrow key twice to move the molecules apart. Arrow keys move the model in space. This movement differs from the movement of the observation point by mouse, since it changes atom coordinates, while the mouse-driven movements change our view on the model without changing the model. Press the Home button (a similar button can be found in the toolbar) to direct the line of sight along the Z axis, so that the X and Y axes become horizontal and vertical, respectively. Press the space bar to position the whole model in the window center without changing the line of sight. At this stage the water molecule is not yet integrated into the model; to hightlight this it is shown as dark spheres reduced in size. Checking the No overlap option erases the molecules considerably overlapping with the current model. If everything is correct, press the OK button, which includes this water molecule to the model and gives the water molecule a normal appearance. Otherwise, pressing the Cancel button undoes the Add command and erases the previewed (gray) molecule from screen. Save the intermediate model (File > Save as... newfile.hin). Now let us duplicate the model several times and change its orientation to arrange the molecules on a regular lattice. To do so, select the newfile.hin in the File > Add menu. No changes are visible in the graphical window since the molecules are perfectly aligned. Set the rotation angle to 180° and rotate the model about the Z axis (right lower button). Shift the model 6 Å right and 6 Å up. Confirm the new model (OK button) and save it (File > Save as... newfile.hin). Add a new copy of the model, rotate it 90° about the Z axis (right lower button), and shift 6 Å right and 6 Å up. This yields a cube of 8 molecules. A big box for molecular dynamics can be generated using the Edit > Build crystal menu. Switch on the Preview mode on the emerged panel. Dark copies of the model appear. They are not yet valid as in the case of using the Add command. Set Cell copies equal to 3 and make sure there is no considerable overlapping of the molecules. Switch off the Preview mode and press the Expand button. Several seconds later, a box containing 216 solvent molecules appears. It is not recommended to make more than 10 model copies at once. It may take lots of time. Instead, generate the box in several steps. Now let us proceed to molecular dynamics (Compute > Protocol menu). Select the '! MDynaMix' protocol and press the Options button. The control panel of the MDynaMix program appears: Check the Box option in the Boundary conditions section. Now you can manually set the periodic boundary conditions (PBC) box size. Instead, select the box size to match the corresponding lattice parameters in the Crystal builder by checking the From crystal option . Now everything is ready to start the molecular dynamics algorithm. First, the model should be brought into an equilibrium state. The '! MDynaMix' protocol includes several equilibration steps. The '0.2 ps at 10 K' simulation is aimed to eliminate too close contacts between atoms, which can be present in the initial raw model. The '2 ps at 25°' simulation suffices to reach the desired mean temperature. The final equilibration steps include the '20 ps at 25°' simulation at constant volume and the '20 ps at 100 atm' and '100 ps at 1 atm' simulations. Next, the production step ('100 ps productive simulation') is executed. This is a raw protocol that can be recommended for demonstrations and generation of crude models to be used in the following longer simulations. Start the simulation by pressing the Run button. Now you can observe molecular motion on the screen. The bottom line shows current time step, different contribution to the energy, temperature, pressure and density. Graph plotting can be accessed by double-clicking the desired monitor in the Analyze > Monitor menu: Protocol parameters can be changed by double-clicking the corresponding cell and entering the desired value and/or unit of measurement. For instance, entering '1atm' into the pressure (P) cell sets the constant pressure of 1 atm. Checking the Read option in the Restart section of the MDynaMix control panel forces the following simulation to continue the previous one. With such option, the atomic velocities and box size are inherited from the previous calculation. Set the simulation duration to 20 ps and start the molecular dynamics (Run). If the simulation is performed at constant pressure, make sure that the Read > Restart option is checked in all subsequent simulations. Otherwise, the size of the periodic boundary conditions will be wrong, since it will be reset from the Boundary conditions section.
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| Copyright 1996, 1999, 2005, 2007 by: Alexander Lyubartsev, Aatto Laaksonen, Alexey Nikitin. Department of Physical Chemistry, Stockholm University. All rights reserved. Copyright 2006, 2007 Agile Molecule. All rights reserved.