exercises:2015_ethz_mmm:alanine_dipeptide
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exercises:2015_ethz_mmm:alanine_dipeptide [2015/02/06 17:49] – external edit 127.0.0.1 | exercises:2015_ethz_mmm:alanine_dipeptide [2015/02/27 07:58] – dpasserone | ||
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In this exercise you will obtain a simplified version of the above potential energy surface, obtained in a very similar way as in the paper. You will constrain the angles at fixed values using a strong harmonic potential, and optimize all other degrees of freedom. From this, a grid of energies will be built, and the energy diagram (Ramachandran plot) will be constructed. | In this exercise you will obtain a simplified version of the above potential energy surface, obtained in a very similar way as in the paper. You will constrain the angles at fixed values using a strong harmonic potential, and optimize all other degrees of freedom. From this, a grid of energies will be built, and the energy diagram (Ramachandran plot) will be constructed. | ||
- | <note tip> Create a new directory for this exercise, and copy there the files (** all commented **) that you can download from the wiki: {{exercise_2.2.zip|exercise_2.2.zip}}</ | + | Download |
< | < | ||
- | you@brutusX | + | you@eulerX |
- | you@brutusX | + | you@eulerX |
- | you@brutusX mmm_exercise_2.2$ cp / | + | </ |
+ | |||
+ | <note tip> All files of this exercise (** input and scripts are all commented **) can be downloaded from the wiki: {{exercise_2.2.zip|exercise_2.2.zip}}< | ||
+ | |||
+ | Then go to the directory “exercise_2.2/” | ||
+ | < | ||
+ | you@brutusX ~$ cd exercise_2.2 | ||
</ | </ | ||
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< | < | ||
- | you@brutusX | + | you@brutusX |
- | you@brutusX | + | you@brutusX |
</ | </ | ||
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< | < | ||
- | you@brutusX | + | you@brutusX |
</ | </ | ||
+ | <note important> | ||
+ | Changing into the directory **Logs** you fill find files of the kind **opt.? | ||
+ | m_pdbtorsion: | ||
+ | < | ||
+ | you@brutusX exercise_2.2/ | ||
+ | </ | ||
+ | |||
+ | for the two dihedral **Phi** and **Psi**. | ||
+ | |||
+ | |||
+ | </ | ||
To clean the output and unnecessary files and do it again, | To clean the output and unnecessary files and do it again, | ||
< | < | ||
- | you@brutusX | + | you@brutusX |
</ | </ |
exercises/2015_ethz_mmm/alanine_dipeptide.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1