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 carboxylate is replaced by an acyl group (C-terminus) and the primary amine is converted into a secondary amine by the addition of a methyl group (N-terminus).
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.
a1a2ene.pdbwith 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.
geo.inare missing. Replace
I4by the atomic indices determined previously. Note: While VMD starts counting atoms from 0, CP2K starts counting from 1, i.e. the VMD indices need to be increased by 1.
perform-gopt.shto perform the grid of geometry optimizations.
epot.gp). Which are the two most favoured conformations?