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--- exercise:mm_uzh:alanine_dipeptide [2014/05/19 22:39] – talirz
+++ exercises:2014_uzh_molsim:alanine_dipeptide [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 5: / Line 5: @@
 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.
-{{ :exercise:mm_uzh:alanine.png?direct&400 |}}
+{{ alanine.png?direct&400 |}}
 <note>**TASK 1**
@@ Line 19: / 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. Which are the two most favoured conformations?
+  - 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>