exercises:2017_uzh_cmest:path_optimization_neb
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exercises:2017_uzh_cmest:path_optimization_neb [2017/10/23 11:04] – created tmueller | exercises:2017_uzh_cmest:path_optimization_neb [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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======= Path optimization using NEB ======= | ======= Path optimization using NEB ======= | ||
- | In the [[geometry_optimization|last | + | In one of the [[geometry_optimization|last |
In this exercise, we will therefore perform Nudged Elastic Band (NEB) calculations using the same molecule as before and investigate the energy path between the two geometries. | In this exercise, we will therefore perform Nudged Elastic Band (NEB) calculations using the same molecule as before and investigate the energy path between the two geometries. | ||
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< | < | ||
- | $ nohup mpirun -np 8 cp2k.popt -i ethane_neb_aba.inp -o ethane_neb_aba.out & | + | $ nohup mpirun -np 4 cp2k.popt -i ethane_neb_aba.inp -o ethane_neb_aba.out & |
</ | </ | ||
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</ | </ | ||
- | We replaced the CP2K executable '' | + | We replaced the CP2K executable '' |
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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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 a conformer is stable or not. | + | 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/2017_uzh_cmest/path_optimization_neb.1508756667.txt.gz · Last modified: 2020/08/21 10:15 (external edit)