exercises:2014_ethz_mmm:md_slab
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exercise:md_slab [2014/03/13 16:15] – dpasserone | exercise:md_slab [2014/06/10 00:37] – dpasserone | ||
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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(r) at various temperatures. | 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(r) at various temperatures. | ||
- | As usual, create a new directory and copy the files from: | + | As usual, create a new directory and download |
- | + | ||
- | **/ | + | |
First, we simulate the system at 700 K. Using the file 700.inp, we run a NVT simulation using a thermostat. | First, we simulate the system at 700 K. Using the file 700.inp, we run a NVT simulation using a thermostat. | ||
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- Copy histo_z into another file and modify it to only include the particles from the first 10 frames of the trajectory. | - Copy histo_z into another file and modify it to only include the particles from the first 10 frames of the trajectory. | ||
- Run it and see the differences to the first profile. | - Run it and see the differences to the first profile. | ||
- | | + | - Do the same excluding the first 10 frames. |
- Explain those differences, | - Explain those differences, | ||
</ | </ | ||
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you can (assignment): | you can (assignment): | ||
- | | + | <note important> |
- | - draw the box: **draw pbcbox** in the Tk console | + | - source a pbc.vmd file which includes the definition of the periodic box |
- | - wrap all atoms in the periodic box: **pbc wrap -first first -last last** | + | - draw the box: **draw pbcbox** in the Tk console |
- | - " | + | - wrap all atoms in the periodic box: **pbc wrap -first first -last last** |
- | - Using the " | + | - " |
+ | - Using the " | ||
</ | </ | ||
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exercises/2014_ethz_mmm/md_slab.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1