exercises:2021_uzh_acpc2:ex01
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exercises:2021_uzh_acpc2:ex01 [2021/04/26 07:23] – [Part II: Force Field Parameter] mrossmannek | exercises:2021_uzh_acpc2:ex01 [2021/04/26 07:40] – [Part IV: Ensembles] mrossmannek | ||
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- | ===== Part III: Radial distribution | + | ===== Part III: Radial distribution |
+ | In this section we analyze the dependence of the radial distribution function (rdf), $g(r)$, on the temperature of the system. To do so, you should plot $g(r)$ against various temperatures and examine the effects. | ||
+ | You can use VMD (as explained below) or write your own program (Fortran, C, C++, Python etc.) to calculate the rdf. | ||
- | Use VMD or write your own program (Fortran, C, C++, Python etc.) to calculate radial distribution $g(r)$. Plot $g(r)$, and against various the temperatures to examine the effects. | + | VMD comes with an extension for exactly this purpose: In the VMD Main window open “Extensions → Analysis” click on “Radial Pair Distribution function $g(r)$“. In the appearing window use “Utilities → Set unit cell dimensions” to tell VMD the size of the simulation box you used. After that use Selection 1 and 2 to define the atomic types that you want to calculate the rdf for, for example “element Ar”. In the plot window, use the " |
- | VMD comes with an extension for exactly this purpose: In the VMD Main window open “Extensions → Analysis” click on “Radial Pair Distribution function $g(r)$. In the appearing window use “Utilities → Set unit cell dimensions” to let VMD know the simulation box you used. After that use Selection 1 and 2 to define the atomic types that you want to calculate the rdf for, for example “element Ar”. In the plot window, use " | + | |
< | < | ||
* Plot $g(r)$ at 84, 300 and 400 K into the same graph. | * Plot $g(r)$ at 84, 300 and 400 K into the same graph. | ||
- | * What are the differences in the height of the first peak, and why does temperature contribute to the differences? | + | * What are the differences in the height of the first peak, and why/how does the temperature contribute to the differences? |
- | * Compared | + | * Compare your results |
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<code - exp_gr.dat> | <code - exp_gr.dat> | ||
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- | ===== Part IV: Ensembles | + | ===== Part IV: Other Ensembles |
- | In previous | + | In the previous |
- | Step up NVT calculation, | + | To set up an NVT calculation, |
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- | Step up NPT calculation, | + | To set up an NPT calculation, |
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**TASK** | **TASK** | ||
- | *Run calculation using NVT at 300K, check the temperature, and energy of the whole system, and compare the result to NVE (300K), and rationalize | + | |
- | *Run calculation using NVT (300K) until the system is equilibrated then run NVE, check the temperature, and energy of the whole system, and compare to previous NVE simulation. | + | |
- | | + | |
exercises/2021_uzh_acpc2/ex01.txt · Last modified: 2021/05/17 11:35 by mrossmannek