exercises:2018_uzh_cmest:path_optimization_neb
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exercises:2018_uzh_cmest:path_optimization_neb [2018/10/23 14:06] – [Path optimization using NEB] abussy | exercises:2018_uzh_cmest:path_optimization_neb [2018/10/24 10:30] – [Vibrational analysis] abussy | ||
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- | Note the use of "mpirun -np 4" | + | Note the use of '' |
This may take a couple of hours. Continue with the exercises below once the calculation finishes. | This may take a couple of hours. Continue with the exercises below once the calculation finishes. | ||
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- | Once this run completes, | + | Once this run completes, you can grep for the modes frequency with: |
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- | Now we are going to use the application //molden// (which | + | |
< | < | ||
- | $ molden | + | $ grep " |
</ | </ | ||
- | Click the //Norm. Mode// checkbox in the //Molden Control// window to list all the modes. What is the lowest frequency you get? By clicking on it you can visualize it. | + | The presence of a negative (imaginary) mode means that it is actually a transition state (and not stable). |
- | + | ||
- | The presence of a negative (imaginary) mode means that it is actually a transition state (and not stable). | + | |
Now repeat the same steps presented here for the bead with the lowest energy. What is now the first frequency you get in the list? Is this geometry stable? | Now repeat the same steps presented here for the bead with the lowest energy. What is now the first frequency you get in the list? Is this geometry stable? | ||
- | Please note: while you should get only 18 different frequencies you get 21 instead. That means that 3 frequencies are global rotations instead of modes in the molecule and should be ignored when looking for negative frequencies to identify whether | + | Note that cp2k also produces |
exercises/2018_uzh_cmest/path_optimization_neb.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1