CP2K Open Source Molecular Dynamics

User Tools

Site Tools

Trace:
exercises:2014_uzh_molsim:alanine_dipeptide

Differences

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

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
exercise:mm_uzh:alanine_dipeptide [2014/06/11 11:43] – talirzexercises:2014_uzh_molsim:alanine_dipeptide [2020/08/21 10:15] (current) – external edit 127.0.0.1
Line 8: Line 8:
 the torsional angle $\phi$ is C-N-C-C, while $\psi$ is N-C-C-N along the backbone. 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** <note>**TASK 1**
Line 19: Line 19:
 <note>**TASK 2** <note>**TASK 2**
  
-  - Enter the input file ''geo.in'' and replace the dummy indices to define the dihedral angles. //Note:// While VMD starts counting atoms from 0, CP2K starts counting from 1. In order for CP2K to select the correct atoms, you will need to increase the VMD indices 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. //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 ''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]].   - Compare with Figure 3 of [[doi>10.1073/pnas.100127697]].
 </note> </note>
exercises/2014_uzh_molsim/alanine_dipeptide.1402487006.txt.gz · Last modified: 2020/08/21 10:14 (external edit)