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--- exercises:2018_uzh_acpc2:mol_sol [2018/05/08 11:12] – [Ramachandran plot] jglan
+++ exercises:2018_uzh_acpc2:mol_sol [2018/05/08 11:13] – [Ramachandran plot] jglan
@@ Line 87: / Line 87: @@
 </note>
-<note important>The index number in VMD is different from the number in CP2K, as the index start from 0 in VMD, 1 in CP2K. Thus, one need to specify index number + 1 obtained from VMD</note>
+<note important>//Note:// While VMD starts counting atoms from 0, CP2K starts counting from 1, i.e. the VMD indices need to be increased by 1.</note>
@@ Line 95: / Line 95: @@
 <note>**TASK 2**
-  - 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.
+  - 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.
   - Use ''perform-gopt.sh'' to perform the grid of geometry optimizations.
   - Use gnuplot to plot the potential energy surface (we have provided a script ''epot.gp''). Which are the two most favoured conformations? <code> $ gnuplot</code><code> gnuplot > load "epot.gp"</code>
 </note>
 ===== Glyala in water =====
 Now, we will move to a more realistic system - Glyala in water. We will preformed a MD of glyala in water and save the trajectory.