exercises:2014_uzh_molsim:alanine_dipeptide
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exercise:mm_uzh:alanine_dipeptide [2014/05/19 21:29] – talirz | exercises:2014_uzh_molsim:alanine_dipeptide [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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The conformations of alanine dipeptide are characterized by the dihedral angles of the backbone. | The conformations of alanine dipeptide are characterized by the dihedral angles of the backbone. | ||
- | Below, we color carbons in blue, hydrogens in white, oxygen in red and nitrogen in blue, i.e. | + | Below, we color carbons in green, hydrogens in white, oxygen in red and nitrogen in blue, i.e. |
the torsional angle $\phi$ is C-N-C-C, while $\psi$ is N-C-C-N along the backbone. | the torsional angle $\phi$ is C-N-C-C, while $\psi$ is N-C-C-N along the backbone. | ||
- | {{ : | + | {{ alanine.png? |
< | < | ||
- | Visualize the structure '' | + | Visualize the structure '' |
</ | </ | ||
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< | < | ||
- | - Enter the input file '' | + | - The atomic indices defining the dihedral indices in the input file '' |
- Use '' | - Use '' | ||
- | - Use '' | + | - Use gnuplot to plot the potential energy surface (we have provided a script |
+ | - Compare with Figure 3 of [[doi> | ||
</ | </ | ||
- |
exercises/2014_uzh_molsim/alanine_dipeptide.1400534968.txt.gz · Last modified: 2020/08/21 10:14 (external edit)