Differences

This shows you the differences between two versions of the page.

--- exercise:mm_uzh:alanine_dipeptide [2014/05/19 21:22] – created talirz
+++ exercises:2014_uzh_molsim:alanine_dipeptide [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-====== Potential energy surface of 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//.
-Alanine dipeptide has more than one long-lived conformation, which are characterized by the dihedral angles of the backbone.
+The conformations of alanine dipeptide are characterized by the dihedral angles of the backbone.
-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.
-{{ :exercise:mm_uzh:alanine.png?direct&400 |}}
+{{ alanine.png?direct&400 |}}
-In this exercise, we are going to map out the potential energy surface of alanine dipeptide
-as a function of the dihedral angles $\phi$ and $\psi$.
 <note>**TASK 1**
-Visualize the structure ''alanine.pdb'' with VMD and determine the atomic indices of the atoms defining the dihedral angles.
+Visualize the structure ''a1a2ene.pdb'' with VMD and determine the atomic indices of the atoms defining the dihedral angles.
 </note>
@@ Line 21: / Line 19: @@
 <note>**TASK 2**
-  - Enter the input file ''geo.in'' and define the dihedral angles
+  - The atomic indices defining the dihedral indices in the input file ''geo.in'' are missing. Replace ''I1'' to ''I4'' by 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.
   - Use ''perform-gopt.sh'' to perform the grid of geometry optimizations.
-  - Use ''epot.gp'' to plot your results
+  - Use gnuplot to plot the potential energy surface (we have provided a script ''epot.gp''). Which are the two most favoured conformations?
+  - Compare with Figure 3 of [[doi>10.1073/pnas.100127697]].
 </note>