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exercises:2019_uzh_acpc2:ex03

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exercises:2019_uzh_acpc2:ex03 [2019/05/13 23:51] – keimreexercises:2019_uzh_acpc2:ex03 [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 $$ \text{Cl}^- + \text{CH}_3\text{Cl} \longleftrightarrow \text{Cl}\text{CH}_3 + \text{Cl}^-. $$ $$ \text{Cl}^- + \text{CH}_3\text{Cl} \longleftrightarrow \text{Cl}\text{CH}_3 + \text{Cl}^-. $$
  
-For energy and force evaluation, we will use the Parameterization Method 6 (PM6), which is a relatively inexpensive semiempirical model for electronic structure. For accurate reaction characterizations, ab initio methods, such as DFT or higher, should be used.+For energy and force evaluation, we will use the Parameterization Method 6 (PM6), which is a relatively inexpensive semiempirical model for electronic structure evaluation. For accurate reaction characterizations, ab initio methods, such as DFT or higher level, should be used.
  
 ===== NEB activation barrier ===== ===== NEB activation barrier =====
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 === Geometry optimizations === === Geometry optimizations ===
  
-To start the NEB calculation, we first need two geometries of the local minima, which we can obtain by running geometry optimization calculations. Use the following CP2K input script to obtain the first geometry:+To start the NEB calculation, we first need two different geometries at local energy minima, which we can obtain by running geometry optimization calculations. Use the following CP2K input script to obtain the first geometry:
  
 <code - geo.inp> <code - geo.inp>
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 </code> </code>
  
-In the main output of the NEB calculation, you will find the following type of sections:+In the main output of the NEB calculation, you will find a number of the following sections:
 <code> <code>
 ******************************************************************************* *******************************************************************************
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  *******************************************************************************  *******************************************************************************
 </code> </code>
-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.
  
 <note>**TASK 2** <note>**TASK 2**
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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, parallel tempering, ...) have to be used. However, for our simple $S_N2$ reaction, we will use unbiased Molecular Dynamics (MD).  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, parallel tempering, ...) have to be used. However, for our simple $S_N2$ reaction, we will use unbiased Molecular Dynamics (MD). 
  
-The FES is a projection of the high-dimensional free energy landscape usually into two dimensions. These two dimensions are called collective variables (CV) and they must be chosen such that various stable conformations can be distinguished and the reaction pathways can be adequately described by the FES. For complex systems, the choice of CVs is a non-trivial task. Fortunately for our simple system, the choice is simple: we take the distances of the two Cl anions from the central C as the CVs.+The FES is a projection of the high-dimensional free energy landscape into a small number, usually two, dimensions. These two dimensions are called collective variables (CV) and they must be chosen such that various stable conformations can be distinguished and the reaction pathways can be adequately described by the FES. For complex systems, the choice of CVs is a non-trivial task. Fortunately for our simple system, the choice is simple: we take the distances of the two Cl anions from the central C as the CVs.
  
-To help the system sample the parts of FES we care about, we will include restraints in the MD calculation, which prevents the Cl anions from going too far from the molecule.+To help the calculation sample the parts of FES we care about, we will include restraints in the MD run, which prevent the Cl anions from going too far from the molecule.
  
 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 ''ch3f-COLVAR.metadynLog'' file produced by the MD run. (Don't forget to change the temperature!)+The following Python script can be used to calculate the FES from the ''ch3f-COLVAR.metadynLog'' file produced by the MD run. (Don't forget to change the temperature in Python script!)
  
 <code> <code>
 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                          #Change temperature according to your MD simulations!
 colvar_path = "./ch3f-COLVAR.metadynLog" colvar_path = "./ch3f-COLVAR.metadynLog"
  
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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? What are the reaction 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> </note>
- 
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