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--- exercises:2015_ethz_mmm:alanine_dipeptide [2015/02/06 17:49] – external edit 127.0.0.1
+++ exercises:2015_ethz_mmm:alanine_dipeptide [2015/02/27 09:02] – yakutovich
@@ Line 13: / Line 13: @@
 In this exercise you will obtain a simplified version of the above potential energy surface, obtained in a very similar way as in the paper. You will constrain the angles at fixed values using a strong harmonic potential, and optimize all other degrees of freedom. From this, a grid of energies will be built, and the energy diagram (Ramachandran plot) will be constructed.
-<note tip> Create a new directory for this exercise, and copy there the files (** all commented **) that you can download from the wiki: {{exercise_2.2.zip|exercise_2.2.zip}}</note>
+Download the 2.2 exercise into your $HOME folder and unzip it.
 <code>
-you@brutusX ~$ mkdir mmm_exercise_2.2
+you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_2.2.zip
-you@brutusX ~$ cd mmm_exercise_2.2
+you@eulerX ~$ unzip exercises:2015_ethz_mmm:exercise_2.2.zip
-you@brutusX mmm_exercise_2.2$ cp /cluster/home03/matl/danielep/LECTURE2/EXERCISE_2.2/* .
+</code>
+<note tip> All files of this exercise (** input and scripts are all commented **) can be downloaded from the wiki: {{exercise_2.2.zip|exercise_2.2.zip}}</note>
+Then go to the directory “exercise_2.2/”
+<code>
+you@eulerX ~$ cd exercise_2.2
 </code>
@@ Line 133: / Line 139: @@
 <code>
-you@brutusX mmm_exercise_2.2$ module load cp2k/trunk.2.5.13191
+you@eulerX exercise_2.2$ module load new cp2k
-you@brutusX mmm_exercise_2.2$ bsub < grid_brutus
+you@eulerX exercise_2.2$ bsub < grid_alanine
 </code>
@@ Line 141: / Line 147: @@
 <code>
-you@brutusX mmm_exercise_2.2$ gnuplot dihedral.gnu
+you@eulerX exercise_2.2$ gnuplot torsion.gnu
 </code>
+<note important>
+Changing into the directory **Logs** you fill find files of the kind **opt.?.?.pdb** . You can now verify that the target torsional angles have been reached. To this end you can either use the graphical program **vmd** (first, load the module with **module load vmd**) or the function
+m_pdbtorsion:
+<code>
+you@eulerX exercise_2.2/Logs$ m_pdbtorsion 5 7 9 15 ; m_pdbtorsion 7 9 15 17
+</code>
+for the two dihedral **Phi** and **Psi**.
+</note>
 To clean the output and unnecessary files and do it again,
 <code>
-you@brutusX mmm_exercise_2.2$ ./cleanall
+you@eulerX exercise_2.2$ ./cleanall
 </code>