exercises:2015_cecam_tutorial:mtd1
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exercises:2015_cecam_tutorial:mtd1 [2015/08/19 12:56] – fix file links tmueller | exercises:2015_cecam_tutorial:mtd1 [2015/08/19 14:58] – add original author and link to data file tmueller | ||
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Problem: Dissociation reaction of nitric acid on graphene and atomic rearrangements of a < | Problem: Dissociation reaction of nitric acid on graphene and atomic rearrangements of a < | ||
- | ======= Introduction | + | * Original author: Marcella Iannuzzi |
+ | * Complete source and output files: [[http:// | ||
+ | ===== Introduction ===== | ||
For this tutorial some input and output files are given in order to present a complete procedure to solve the given problem. Some hints are also given to help in the analysis of the results. In order to be able to run these examples, some paths need to be correctly set in the input files (i.e. set the variables '' | For this tutorial some input and output files are given in order to present a complete procedure to solve the given problem. Some hints are also given to help in the analysis of the results. In order to be able to run these examples, some paths need to be correctly set in the input files (i.e. set the variables '' | ||
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* Metadynamics simulation aimed at observing atomic rearrangements of the cluster bay changing the coordination of both Si and H species. | * Metadynamics simulation aimed at observing atomic rearrangements of the cluster bay changing the coordination of both Si and H species. | ||
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- | ======= First task: dynamics of two HNO3 molecules over a graphene sheet ======= | + | ===== First task: dynamics of two HNO3 molecules over a graphene sheet ===== |
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The examples on this system are in the directory '' | The examples on this system are in the directory '' | ||
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By plotting the CV as recorded along the short MD trajectory (3 ps), the amplitude of the equilibrium fluctuations can be evaluated and then used to set up the size of the Gaussian hills that build up the biasing potential. The first CV fluctuates close to zero, with fluctuations smaller than 0.2. The second is around 2.8. The fluctuations are smaller due to the stiffness of the three NO bonds. The coordination of H to C is also typically zero, but it can change a lot when the molecules approach the layer, even if there is no dissociation of H and no binding to C. This indicates that this variable is difficult to control and might turn out to be tricky to use it to distinguish among different states of the reaction process. The point to plane distance shows quite large fluctuations and it is clearly not suited to distinguish a specific state along the reaction path. Moreover, its minima, when the two molecules are closer to the layer, correspond to the maxima of the third CV, i.e. the CN of H to C. At least before dissociation, | By plotting the CV as recorded along the short MD trajectory (3 ps), the amplitude of the equilibrium fluctuations can be evaluated and then used to set up the size of the Gaussian hills that build up the biasing potential. The first CV fluctuates close to zero, with fluctuations smaller than 0.2. The second is around 2.8. The fluctuations are smaller due to the stiffness of the three NO bonds. The coordination of H to C is also typically zero, but it can change a lot when the molecules approach the layer, even if there is no dissociation of H and no binding to C. This indicates that this variable is difficult to control and might turn out to be tricky to use it to distinguish among different states of the reaction process. The point to plane distance shows quite large fluctuations and it is clearly not suited to distinguish a specific state along the reaction path. Moreover, its minima, when the two molecules are closer to the layer, correspond to the maxima of the third CV, i.e. the CN of H to C. At least before dissociation, | ||
- | ======= Second task: Metadynamics of the dissociation of HNO3 over a graphene sheet ======= | + | ===== Second task: Metadynamics of the dissociation of HNO3 over a graphene sheet ===== |
The presented MTD run employs as CV only the three CN described above. The related input file is '' | The presented MTD run employs as CV only the three CN described above. The related input file is '' | ||
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Other quantities that can be monitored from the '' | Other quantities that can be monitored from the '' | ||
- | ======= Third task: dynamics of Si6H8 ======= | + | ===== Third task: dynamics of Si6H8 ===== |
The data file for this example are in '' | The data file for this example are in '' | ||
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The dynamics of the CVs along the two simulations, | The dynamics of the CVs along the two simulations, | ||
- | ======= Fourth task: Lagrangian MTD of the atomic rearrangement of Si6H8 ======= | + | ===== Fourth task: Lagrangian MTD of the atomic rearrangement of Si6H8 ===== |
'' | '' |
exercises/2015_cecam_tutorial/mtd1.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1