exercises:2019_uzh_acpc2:ex03
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exercises:2019_uzh_acpc2:ex03 [2019/05/13 23:53] – keimre | exercises:2019_uzh_acpc2:ex03 [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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=== Geometry optimizations === | === Geometry optimizations === | ||
- | To start the NEB calculation, | + | To start the NEB calculation, |
<code - geo.inp> | <code - geo.inp> | ||
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</ | </ | ||
- | In the main output of the NEB calculation, | + | In the main output of the NEB calculation, |
< | < | ||
******************************************************************************* | ******************************************************************************* | ||
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| | ||
</ | </ | ||
- | The sections show for every replica geometry along the NEB trajectory, the distance to its neighbors and its energy. The final section corresponds to the converged NEB trajectory. | + | These sections show for every replica geometry along the NEB trajectory, the distance to its neighbors and its energy. The final section corresponds to the converged NEB trajectory. |
< | < | ||
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Sampling the free energy surface (FES) of a chemical system is a convenient method to explore various stable conformations and possible reaction pathways. To calculate the FES for complicated systems, advanced sampling methods (such as umbrella sampling, metadynamics, | Sampling the free energy surface (FES) of a chemical system is a convenient method to explore various stable conformations and possible reaction pathways. To calculate the FES for complicated systems, advanced sampling methods (such as umbrella sampling, metadynamics, | ||
- | The FES is a projection of the high-dimensional free energy landscape | + | The FES is a projection of the high-dimensional free energy landscape into a small number, usually |
- | To help the system | + | To help the calculation |
The following CP2K input script runs our MD calculation and prints out the CV values for every step: | The following CP2K input script runs our MD calculation and prints out the CV values for every step: | ||
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where $s$ is the set CVs and $P(s)$ is the probability that the system has the set of CV values $s$. | where $s$ is the set CVs and $P(s)$ is the probability that the system has the set of CV values $s$. | ||
- | The following Python script can be used to calculate the FES from the '' | + | The following Python script can be used to calculate the FES from the '' |
< | < | ||
import numpy as np | import numpy as np | ||
import matplotlib.pyplot as plt | import matplotlib.pyplot as plt | ||
- | import ase | ||
bohr_2_angstrom = 0.529177 | bohr_2_angstrom = 0.529177 | ||
kb = 8.6173303e-5 # eV * K^-1 | kb = 8.6173303e-5 # eV * K^-1 | ||
- | temperature = 1000.0 | + | temperature = 1000.0 |
colvar_path = " | colvar_path = " | ||
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* Run the MD calculation for 400K, 800K, 1200K and 1600K. (The calculations can a take a while.) | * Run the MD calculation for 400K, 800K, 1200K and 1600K. (The calculations can a take a while.) | ||
* 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? | + | * In general, how does potential energy differ from free energy? |
</ | </ | ||
- |
exercises/2019_uzh_acpc2/ex03.1557791613.txt.gz · Last modified: 2020/08/21 10:15 (external edit)