# Open SourceMolecular Dynamics

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exercises:2017_uzh_cmest:path_optimization_neb

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 exercises:2017_uzh_cmest:path_optimization_neb [2017/10/23 11:04]tmueller created exercises:2017_uzh_cmest:path_optimization_neb [2018/01/25 20:24]jglan 2018/01/25 20:24 jglan 2017/10/23 12:01 tmueller 2017/10/23 11:04 tmueller created Next revision Previous revision 2018/01/25 20:24 jglan 2017/10/23 12:01 tmueller 2017/10/23 11:04 tmueller created Line 1: Line 1: ======= Path optimization using NEB ======= ======= Path optimization using NEB ======= - In the [[geometry_optimization|last ​exercise]] you have calculated the energy for Ethane for two slightly different geometries and noticed that the geometry optimization was not able to change one structure into the other with lower energy. As presented in the lecture, it may happen quiet often that a minimization algorithm gets stuck in a local minimum, respectively it is not guaranteed to find the global minimum. + In one of the [[geometry_optimization|last ​exercises]] you calculated the energy for Ethane for two slightly different geometries and noticed that the geometry optimization was not able to change one structure into the other with lower energy. As presented in the lecture, it may happen quiet often that a minimization algorithm gets stuck in a local minimum, respectively it is not guaranteed to find the global minimum. 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. Line 158: Line 158: <​code>​ <​code>​ - $nohup mpirun -np 8 cp2k.popt -i ethane_neb_aba.inp -o ethane_neb_aba.out & +$ nohup mpirun -np 4 cp2k.popt -i ethane_neb_aba.inp -o ethane_neb_aba.out & ​ Line 173: Line 173: ​ - We replaced the CP2K executable ''​cp2k.sopt''​ with ''​cp2k.popt'',​ which is a parallel version of CP2K. By prefixing the command with ''​mpirun -np 8''​ we tell it to run it using the MPI system using 8 cores. And finally to have the command continue to run even if you log out, we prefixed everything with ''​nohup''​. The ampersand ''&''​ at the end is to run everything in the background. + We replaced the CP2K executable ''​cp2k.sopt''​ with ''​cp2k.popt'',​ which is a parallel version of CP2K. By prefixing the command with ''​mpirun -np 4''​ we tell it to run it using the MPI system using 4 cores. And finally to have the command continue to run even if you log out, we prefixed everything with ''​nohup''​. The ampersand ''&''​ at the end is to run everything in the background. 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. Line 314: Line 314: 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.