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exercises:2014_ethz_mmm:alanine_dipeptide

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exercises:2014_ethz_mmm:alanine_dipeptide [2014/10/15 13:26]
oschuett
exercises:2014_ethz_mmm:alanine_dipeptide [2014/10/15 13:27] (current)
oschuett
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 A detailed study of this system (see [[doi>​10.1073/​pnas.100127697]]) shows the presence, in vacuum of two stable states: A detailed study of this system (see [[doi>​10.1073/​pnas.100127697]]) shows the presence, in vacuum of two stable states:
  
-{{ :exercise:screen_shot_2014-02-26_at_9.38.21_am.png?​direct&​300 |}}+{{ screen_shot_2014-02-26_at_9.38.21_am.png?​direct&​300 |}}
  
 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/​mol. ​ 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/​mol. ​
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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>​+<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}}</​note>​
  
 <​code>​ <​code>​
exercises/2014_ethz_mmm/alanine_dipeptide.txt ยท Last modified: 2014/10/15 13:27 by oschuett