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--- exercises:2015_ethz_mmm:alanine_dipeptide [2015/02/26 15:56] – yakutovich
+++ exercises:2015_ethz_mmm:alanine_dipeptide [2015/02/27 09:02] – yakutovich
@@ Line 24: / Line 24: @@
 Then go to the directory “exercise_2.2/”
 <code>
-you@brutusX ~$ cd exercise_2.2
+you@eulerX ~$ cd exercise_2.2
 </code>
@@ Line 139: / Line 139: @@
 <code>
-you@brutusX exercise_2.2$ module load new cp2k
+you@eulerX exercise_2.2$ module load new cp2k
-you@brutusX exercise_2.2$ bsub < grid_alanine
+you@eulerX exercise_2.2$ bsub < grid_alanine
 </code>
@@ Line 147: / Line 147: @@
 <code>
-you@brutusX exercise_2.2$ gnuplot torsion.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 exercise_2.2$ ./cleanall
+you@eulerX exercise_2.2$ ./cleanall
 </code>