exercises:2021_uzh_acpc2:ex03
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| exercises:2021_uzh_acpc2:ex03 [2021/05/21 08:09] – [Free energy surface] Some improvements mrossmannek | exercises:2021_uzh_acpc2:ex03 [2021/05/21 10:13] (current) – [Free energy surface] Add tip about RuntimeWarning mrossmannek | ||
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| Line 178: | Line 178: | ||
| &GLOBAL | &GLOBAL | ||
| PRINT_LEVEL LOW | PRINT_LEVEL LOW | ||
| - | PROJECT | + | PROJECT |
| RUN_TYPE MD # Molecular Dynamics | RUN_TYPE MD # Molecular Dynamics | ||
| &END GLOBAL | &END GLOBAL | ||
| Line 324: | Line 324: | ||
| * Create the corresponding FES plots and discuss the temperature dependence. | * Create the corresponding FES plots and discuss the temperature dependence. | ||
| * In general, how does potential energy differ from free energy? For our reaction, what are the activation barriers from the different free energy surfaces? How and why do they differ from the NEB barrier? | * In general, how does potential energy differ from free energy? For our reaction, what are the activation barriers from the different free energy surfaces? How and why do they differ from the NEB barrier? | ||
| + | </ | ||
| + | |||
| + | <note tip> | ||
| + | You may encounter a warning like the following: | ||
| + | < | ||
| + | plot.py:24: RuntimeWarning: | ||
| + | fes = -kb * temperature * np.log(prob) | ||
| + | </ | ||
| + | Don't worry about this, the script still works as expected and produces the plot in the file '' | ||
| </ | </ | ||
exercises/2021_uzh_acpc2/ex03.txt · Last modified: 2021/05/21 10:13 by mrossmannek