exercises:2016_uzh_cmest:path_optimization_neb
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exercises:2016_uzh_cmest:path_optimization_neb [2016/10/20 19:39] – [Vibrational analysis] tmueller | exercises:2016_uzh_cmest:path_optimization_neb [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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To verify whether the point at the highest energy is actually a transition state, we will be doing a vibrational analysis. | To verify whether the point at the highest energy is actually a transition state, we will be doing a vibrational analysis. | ||
- | First identify the bead with the highest energy (see exercise above) and create a new XYZ file named '' | + | First identify the bead with the highest energy (see exercise above) and create a new XYZ file named '' |
- | Use the following input file: | + | Use the following input file and the same command as above (with different input and output file names of course) to generate the analysis. |
<code - ethane_TS_va.inp> | <code - ethane_TS_va.inp> | ||
Line 295: | Line 295: | ||
REPLICA_EVAL 1 | REPLICA_EVAL 1 | ||
&END | &END | ||
- | | + | |
&END | &END | ||
&END | &END | ||
</ | </ | ||
+ | |||
+ | Once this run completes, you should find a file '' | ||
+ | |||
+ | Now we are going to use the application //molden// (which you can load using '' | ||
+ | |||
+ | < | ||
+ | $ molden ethane_TS_va-VIBRATIONS-1.mol | ||
+ | </ | ||
+ | |||
+ | 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). | ||
+ | |||
+ | 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 a conformer is stable or not. |
exercises/2016_uzh_cmest/path_optimization_neb.1476992373.txt.gz · Last modified: 2020/08/21 10:15 (external edit)