exercises:2015_ethz_mmm:nacl_md
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exercises:2015_ethz_mmm:nacl_md [2015/02/06 17:49] – external edit 127.0.0.1 | exercises:2015_ethz_mmm:nacl_md [2015/03/26 11:05] – sclelia | ||
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- | ====== | + | ====== |
- | Perform a MD simulation of NaCl in water by running | + | This short task will help you to familiarize with Molecular Dynamics simulations. The simulation |
- | Use VMD to calculate the Na-Cl distance for each frame of the trajectory. | + | * You can perform the simulation of NaCl in water by running the input-file: '' |
+ | |||
+ | <note tip> | ||
+ | You should run this calculation on 4 cores with '' | ||
+ | </ | ||
+ | |||
+ | * Then 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 | ||
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Plot the obtained distance-trajectory. Does the dissociation occur? If it occurs, does the actual transition happens quickly ? Is dissociation a likely or rare event ? Do you expect an activation energy ? | Plot the obtained distance-trajectory. Does the dissociation occur? If it occurs, does the actual transition happens quickly ? Is dissociation a likely or rare event ? Do you expect an activation energy ? | ||
- | <note tip> | + | |
- | You should run this calculation on 4 cores with '' | + | |
- | </ | + | |
====== Required Files ====== | ====== Required Files ====== | ||
+ | The file is divided in 2 parts: | ||
+ | * GLOBAL & MOTION : Specify the parameters of the simulations | ||
+ | * FORCE EVAL : Specifies the system geometry and interactions between atoms | ||
<code - NaCl_in_water.inp> | <code - NaCl_in_water.inp> | ||
&GLOBAL | &GLOBAL | ||
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&END CELL | &END CELL | ||
& | & | ||
+ | Na 1.0978482003279533E+01 | ||
+ | Cl 1.3489457703231567E+01 | ||
O 1.1753544421905696E+01 | O 1.1753544421905696E+01 | ||
H 1.2340708249225194E+01 | H 1.2340708249225194E+01 | ||
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H 1.3706746681864210E+01 | H 1.3706746681864210E+01 | ||
H 1.5269466984949403E+01 | H 1.5269466984949403E+01 | ||
- | Na 1.0978482003279533E+01 | ||
- | Cl 1.3489457703231567E+01 | ||
& | & | ||
& | & | ||
& | & | ||
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& | & | ||
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exercises/2015_ethz_mmm/nacl_md.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1