exercises:2015_pitt:aimd
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exercises:2015_pitt:aimd [2015/03/03 12:07] – [Required files] vondele | exercises:2015_pitt:aimd [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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The second goal to understand the produced .ener file and do some basic analysis of the trajectory with VMD. | The second goal to understand the produced .ener file and do some basic analysis of the trajectory with VMD. | ||
- | ====== AIMD of water ====== | + | ====== AIMD of bulk liquid |
< | < | ||
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How many neighbors does a given water molecule have on average (3, 3-4, 4, 4-5, 5)? | How many neighbors does a given water molecule have on average (3, 3-4, 4, 4-5, 5)? | ||
- | === IR spectrum === | + | ==== IR spectrum |
Based on the time evolution of the dipole of the system, the IR spectral density can be estimated. To estimate the dipole from AIMD, wannier centers need to be computed. This is out of scope of the current tutorial (TODO: find link). We employ a simple approximation, | Based on the time evolution of the dipole of the system, the IR spectral density can be estimated. To estimate the dipole from AIMD, wannier centers need to be computed. This is out of scope of the current tutorial (TODO: find link). We employ a simple approximation, | ||
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< | < | ||
+ | ====== AIMD of simle ions in water solution ====== | ||
===== 4th task: simple ions in solution ===== | ===== 4th task: simple ions in solution ===== | ||
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The easiest way to do so is to replace one or more water molecules (depending on the size of the ion) by the ion in question. Obviously, the configuration produced in this way is far from equilibrium, | The easiest way to do so is to replace one or more water molecules (depending on the size of the ion) by the ion in question. Obviously, the configuration produced in this way is far from equilibrium, | ||
- | Entertaining is to turn one H2O in H+, do you see Eigen and Zundel states and [[wp> | + | Entertaining is to turn one H2O into H+, do you see Eigen and Zundel states and [[wp> |
====== Required files ====== | ====== Required files ====== |
exercises/2015_pitt/aimd.1425384454.txt.gz · Last modified: 2020/08/21 10:14 (external edit)