exercises:2014_ethz_mmm:nacl_md
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exercise:free_energy [2014/05/28 10:59] – [1. Task: Observer NaCl dissociation] oschuett | exercises:2014_ethz_mmm:nacl_md [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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- | ===== 1. Task: Observer NaCl dissociation ===== | + | ====== Observer NaCl dissociation ====== |
Perform a MD simulation of NaCl in water by running the input-file '' | Perform a MD simulation of NaCl in water by running the input-file '' | ||
Use VMD to calculate the Na-Cl distance for each frame of the trajectory. | Use VMD to calculate the Na-Cl distance for each frame of the trajectory. | ||
This can be done in the following way: | This can be done in the following way: | ||
- | - Load the trajectory with VMD. | + | - Load the trajectory with VMD |
- | - Setup the box by typing: | + | - Select '' |
- | - Fold back periodic images by typing: '' | + | - Within the $g(r)$-dialog select |
- | - Select '' | + | - Set the lengths a,b, and c to the value 12.413800, and click '' |
- | - Click successively on the Na and the Cl atom. | + | - Close the $g(r)$-dialog |
- | - Select '' | + | - Fold back periodic images by typing: '' |
- | - Select '' | + | - Select '' |
- | - Go to the tab '' | + | - Click successively on the Na and the Cl atom |
- | - Click '' | + | - Select '' |
+ | - Select '' | ||
+ | - Go to the tab '' | ||
+ | - Click '' | ||
+ | |||
+ | Plot the obtained | ||
+ | <note tip> | ||
+ | You should run this calculation on 4 cores with '' | ||
+ | </ | ||
====== Required Files ====== | ====== Required Files ====== | ||
<code - NaCl_in_water.inp> | <code - NaCl_in_water.inp> | ||
&GLOBAL | &GLOBAL | ||
- | PROJECT | + | PROJECT |
RUN_TYPE MD | RUN_TYPE MD | ||
&END GLOBAL | &END GLOBAL | ||
Line 369: | Line 378: | ||
Cl 1.3489457703231567E+01 | Cl 1.3489457703231567E+01 | ||
& | & | ||
+ | & | ||
+ | & | ||
+ | ATOMS 190 191 | ||
+ | & | ||
+ | & | ||
+ | & | ||
+ | &END COLVAR | ||
& | & | ||
CONNECTIVITY GENERATE | CONNECTIVITY GENERATE |
exercises/2014_ethz_mmm/nacl_md.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1