exercises:2015_ethz_mmm:c2h2_bond_energy
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exercises:2015_ethz_mmm:c2h2_bond_energy [2015/02/26 13:28] – yakutovich | exercises:2015_ethz_mmm:c2h2_bond_energy [2015/03/06 02:39] – dpasserone | ||
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====== C2H2 and C2H4 bond energy ====== | ====== C2H2 and C2H4 bond energy ====== | ||
+ | <note warning> | ||
+ | <note warning> | ||
+ | TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | ||
+ | you@eulerX ~$ module load courses mmm ; mmm-init | ||
+ | </ | ||
+ | |||
<note warning> | <note warning> | ||
Before you start it is **ABSOLUTELY NEСESSARY** to update the function library. So from you $HOME directory please run: | Before you start it is **ABSOLUTELY NEСESSARY** to update the function library. So from you $HOME directory please run: | ||
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you@eulerX ~$ ./ | you@eulerX ~$ ./ | ||
</ | </ | ||
+ | ** Pay attention to the output of this program. It may give you some helpful information** | ||
If you don't have the file " | If you don't have the file " | ||
< | < | ||
you@eulerX ~$ unzip update_functionlibrary.zip | you@eulerX ~$ unzip update_functionlibrary.zip | ||
+ | you@eulerX ~$ chmod 755 update_functionlibrary | ||
+ | </ | ||
+ | Or if you are working on the remote computer you can also do the following: | ||
+ | < | ||
+ | you@eulerX ~$ wget http:// | ||
+ | you@eulerX ~$ unzip exercises: | ||
+ | you@eulerX ~$ chmod 755 update_functionlibrary | ||
</ | </ | ||
</ | </ | ||
- | <note important> | + | <note important> |
< | < | ||
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</ | </ | ||
- | **and to submit the job chain:** | + | **and to submit the job:** |
< | < | ||
- | you@eulerX ~$ bsub < c2h2.a.chain | + | you@eulerX ~$ bsub < jobname |
</ | </ | ||
</ | </ | ||
- | Create a new directory for this exercise: | + | Download the 2.1 exercise |
< | < | ||
- | you@eulerX ~$ mkdir mmm_exercise_2.1 | + | you@eulerX ~$ wget http:// |
- | you@eulerX ~$ cd mmm_exercise_2.1 | + | you@eulerX ~$ unzip exercises: |
</ | </ | ||
- | |||
- | |||
- | |||
- | In this exercise you will test the general AMBER force field, which is suitable for a large class of molecules. In this example you will compute the classical energy of a simple acetylene molecule and apply small variations to the C-C bond lengths. | ||
<note tip> | <note tip> | ||
All files of this exercise (**input and scripts are all commented**) can be downloaded from the wiki: {{exercise_2.1.zip|}} | All files of this exercise (**input and scripts are all commented**) can be downloaded from the wiki: {{exercise_2.1.zip|}} | ||
</ | </ | ||
- | Please copy them to your directory. The input file structure of the template is the following: | ||
- | <code - c2h2.amber.inp.templ> | + | In this exercise you will test the general AMBER force field, which is suitable for a large class of molecules. In this example you will compute the classical energy of a simple acetylene molecule and apply small variations to the C-C bond lengths. |
+ | |||
+ | Then go to the directory " | ||
+ | < | ||
+ | you@eulerX ~$ cd exercise_2.1/ | ||
+ | </ | ||
+ | The input file structure of the template is the following: | ||
+ | |||
+ | <code - c2h2.inp.templ> | ||
& | & | ||
METHOD FIST ! Using Molecular Mechanics | METHOD FIST ! Using Molecular Mechanics | ||
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The script to modify the C-C distance in the input and generate the curve is the following: | The script to modify the C-C distance in the input and generate the curve is the following: | ||
- | <code bash c2h2.amber.chain> | + | <code bash c2h2.chain> |
# | # | ||
# task 2.1 C2H2 bond strength | # task 2.1 C2H2 bond strength | ||
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< | < | ||
- | you@brutusX mmm_exercise_2.1$ module load new cp2k | + | you@eulerX c2h2$ module load new cp2k |
- | you@brutusX mmm_exercise_2.1$ bsub < c2h2.a.chain | + | you@eulerX c2h2$ bsub < c2h2.chain |
</ | </ | ||
Line 177: | Line 194: | ||
< | < | ||
- | you@brutusX mmm_exercise_2.1$ gnuplot fit.triple.gnu | + | you@eulerX c2h2$ gnuplot fit.gnu |
</ | </ | ||
- | <code - fit.triple.gnu> | + | <code - fit.gnu> |
# | # | ||
f(x)=k*(x-x0)*(x-x0)+e0 | f(x)=k*(x-x0)*(x-x0)+e0 | ||
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Now, perform the same exercise in another directory for the molecule C2H4. | Now, perform the same exercise in another directory for the molecule C2H4. | ||
+ | < | ||
+ | you@eulerX c2h2$ cd ../c2h4 | ||
+ | </ | ||
- | * The input c2h4.amber.inp.templ is similar to the previous one, only with different project name (C2H4) and coordinates: | + | * The new input c2h4.inp.templ is similar to the previous one, only with different project name (C2H4) and coordinates: |
<code coo.ch4> | <code coo.ch4> | ||
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* The script to modify the bond lengths changes slightly as well | * The script to modify the bond lengths changes slightly as well | ||
- | <code bash c2h4.a.chain> | + | <code bash c2h4.chain> |
# | # | ||
# task 2.2 C2H4 bond strength | # task 2.2 C2H4 bond strength | ||
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<note tip> | <note tip> | ||
- Report the values of the bond length and force constants in all cases. | - Report the values of the bond length and force constants in all cases. | ||
- | - Discuss these values in view of the kind of molecules we are simulating | + | - Discuss these values in view of the kind of molecules we are simulating. |
+ | </ |
exercises/2015_ethz_mmm/c2h2_bond_energy.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1