# Open SourceMolecular Dynamics

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exercises:2014_ethz_mmm:md_slab

# Hot gold

This exercise deals with heating a gold slab, namely the (100) reconstructed that you already simulated last time. The goal is to plot a density profile in the direction orthogonal to the slab, and to compute (using vmd) the radial distribution function g® at various temperatures.

As usual, create a new directory and download the files from the wiki: exercise_4.2.tar.gz

First, we simulate the system at 700 K. Using the file 700.inp, we run a NVT simulation using a thermostat. Then, the obtained xyz trajectory can be analyzed using the script histo_z available in the directory.

./histo_z 700-pos-1.xyz

The output is 700-pos-1.xyz.z, a file with three columns: z, dn/dz, and the progressive integral of this quantity.

1. Explain the profile, and use the third column to draw conclusions about the surface structure.
2. Study the source of the script. Understand its behavior.
3. Copy histo_z into another file and modify it to only include the particles from the first 10 frames of the trajectory.
4. Run it and see the differences to the first profile.
5. Do the same excluding the first 10 frames.
6. Explain those differences, based on what you see in the *.ener file (energies, temperature…).

Perform a simulation at T=1100 K and T=1300 K (files: 1100.inp and 1300.inp).

Discuss the differences in the density profile. What do you expect to see in vmd?

Now, use vmd to look at the trajectories. As you launch vmd, you can (assignment):

- source a pbc.vmd file which includes the definition of the periodic box - draw the box: draw pbcbox in the Tk console - wrap all atoms in the periodic box: pbc wrap -first first -last last - “play” with representations: try to color the surface atoms in one color, the bulk ones in another color. - Using the “radial distribution function” plugin from the extension menu, draw the g® of the system. Discuss it for 700, 1100, and 1300 K.