Differences

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

--- exercise:alanine_modify [2014/03/06 10:46] – dpasserone
+++ exercises:2014_ethz_mmm:alanine_modify [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
 ====== Modification of the dihedral parameters ======
-<note important>The files for this exercise are in /cluster/home03/matl/danielep/LECTURE2/EXERCISE_2.3
+<note important>The ** commented ** files for this exercise can be downloaded from the wiki: {{exercise_2.3.zip|exercise_2.3.zip}}
 The relevant files are:
   - For the non-restrained optimizations to get A and B configurations, inp.a and inp.b
   - For the restrained optimization along a chain, line_ij and inp_ff.templ, respectively the script to generate the "path" and the input file model for cp2k.
-  - For the line simulation with the dihedral parameters modified, (from 1x to 6x)
+  - For the line simulation with the dihedral parameters modified, (from 1x to 6x), ff_multiply_ij and ff_divide_ij.
-  - For the potential with varying parameters for the Psi dihedral angle, pot_psi.templ, that will be used by ff_ij.
+  - For the potential with varying parameters for the Psi dihedral angle, pot_psi.templ, that will be used by ff_multiply_ij and ff_divide_ij.
 </note>
 In this exercise, you are requested to start from the results of exercise 2, and perform the following steps
@@ Line 26: / Line 26: @@
   - <note important>1 Hartree=27.2116 eV=627.509 kcal/mol</note>
   - In this way you will obtain an energy profile joining the two minima (would it be an idea to do a nudged elastic band?).
-  - Now, you can create a new directory, and use a different potential file where a dihedral angle is increased or decreased. This task is performed by the **ff_ij** script file, where you need again to substitute the values of the A and B pairs of angles to interpolate.
+  - Now, you can create a new directory, and use a different potential file where a dihedral angle is increased or decreased. This task is performed by the **ff_multiply_ij** script file, where you need again to substitute the values of the A and B pairs of angles to interpolate.
   - This time different enemol* files will be generated, each for a modified strength of the bond parameters.
-  - Similarly, the ff_divide_ij will generate profiles with the strength divided by 2,3,4... in the files **enediv.2, enediv.3, enediv.4**...
+  - Similarly, the **ff_divide_ij** will generate profiles with the strength divided by 2,3,4... in the files **enediv.2, enediv.3, enediv.4**...
-  - The mod_ff.gnu file will plot all that, and the shape of the harmonic dihedral potential.
+  - The **mod_ff.gnu** file will plot all that, and the shape of the harmonic dihedral potential.
   - How will the line profile change? Why?