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exercises:2014_uzh_molsim:alanine_dipeptide

# Potential energy surface of alanine dipeptide

Alanine dipeptide is one of the simplest molecules that exhibits some important features common to larger biomolecules. In particular, it has more than one long-lived conformation, which we will identify in this exercise by mapping out its potential energy surface.

The conformations of alanine dipeptide are characterized by the dihedral angles of the backbone. 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.

TASK 1 Visualize the structure a1a2ene.pdb with VMD and determine the atomic indices of the atoms defining the dihedral angles.

With this knowledge at hand, we will fix the dihedral angles and perform geometry optimization for all remaining degrees of freedom.