exercises:2014_ethz_mmm:alanine_dipeptide
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exercise:2014_ethz_mmm:alanine_dipeptide [2014/10/15 13:26] – oschuett | exercise:2014_ethz_mmm:alanine_dipeptide [2014/10/15 13:27] – oschuett | ||
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A detailed study of this system (see [[doi> | A detailed study of this system (see [[doi> | ||
- | {{ :exercise:screen_shot_2014-02-26_at_9.38.21_am.png? | + | {{ screen_shot_2014-02-26_at_9.38.21_am.png? |
The diagram represents the contour lines of the molecular energy as a function of the two dihedral angles. Contour lines are separated by 2 kcal/ | The diagram represents the contour lines of the molecular energy as a function of the two dihedral angles. Contour lines are separated by 2 kcal/ | ||
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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:exercise_2.2.zip|exercise_2.2.zip}}</ | + | <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}}</ |
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exercises/2014_ethz_mmm/alanine_dipeptide.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1