exercises:2014_ethz_mmm:alanine_dipeptide
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| exercise:2014_ethz_mmm:alanine_dipeptide [2014/10/15 12:37] – exercise:alanine_dipeptide renamed to exercise:2014_ethz_mmm:alanine_dipeptide oschuett | exercise:2014_ethz_mmm:alanine_dipeptide [2014/10/15 13:27] – oschuett | ||
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| Alanine dipeptide is often studied in theoretical work because it is among the simplest systems to exhibit some of the important features common to biomolecules. It has more than one long-lived conformational state. The relevant angles are the dihedral angles of the backbone, commonly called Φ and Ψ (see figure). In the following scheme, light blue atoms are carbons, white ones are hydrogens, red are oxygens, and blue are nitrogens. So the torsional angle Φ is C-N-C-C and Ψ is N-C-C-N along the backbone. | Alanine dipeptide is often studied in theoretical work because it is among the simplest systems to exhibit some of the important features common to biomolecules. It has more than one long-lived conformational state. The relevant angles are the dihedral angles of the backbone, commonly called Φ and Ψ (see figure). In the following scheme, light blue atoms are carbons, white ones are hydrogens, red are oxygens, and blue are nitrogens. So the torsional angle Φ is C-N-C-C and Ψ is N-C-C-N along the backbone. | ||
| - | {{ :exercise:alanine.png? | + | {{ alanine.png? |
| 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}}</ |
| < | < | ||
exercises/2014_ethz_mmm/alanine_dipeptide.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1