exercises:2015_ethz_mmm:nacl_free_energy
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exercises:2015_ethz_mmm:nacl_free_energy [2015/03/18 16:19] – sclelia | exercises:2015_ethz_mmm:nacl_free_energy [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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===== 1. Task: Potential energy curve (gas phase) ===== | ===== 1. Task: Potential energy curve (gas phase) ===== | ||
This case is very similar to the computation of the Lennard Jones curve (See: [[exercises: | This case is very similar to the computation of the Lennard Jones curve (See: [[exercises: | ||
- | * For this you have to run the input file '' | + | * For this you have to run the input file '' |
* At the end, plot the potential energy dissociation profile of NaCl. | * At the end, plot the potential energy dissociation profile of NaCl. | ||
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For this you have to run constrained MD simulations at 1K for a range of Na-Cl distances. | For this you have to run constrained MD simulations at 1K for a range of Na-Cl distances. | ||
- | * You have to modify the input file in the folloowing | + | * You have to modify the input file in the following |
- Copy the '' | - Copy the '' | ||
- Change the '' | - Change the '' | ||
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* Use the same input as ** Task 2**. | * Use the same input as ** Task 2**. | ||
- | * BUT take the solvated system coordinates from the previous exercise (See: [[exercises: | + | * BUT take the forcefield and the solvated system coordinates from the previous exercise (See: [[exercises: |
* Other slight modifications to your input: | * Other slight modifications to your input: | ||
- | - In the MOTION-CONSTRAINT section | + | - In the MOTION-CONSTRAINT section |
- In the MOTION-MD section set STEPS 100.000 MD and T 350. | - In the MOTION-MD section set STEPS 100.000 MD and T 350. | ||
* Run the simulation in the same way you did for ** Task 2**. | * Run the simulation in the same way you did for ** Task 2**. | ||
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==== Input file for NaCl in gasphase ==== | ==== Input file for NaCl in gasphase ==== | ||
+ | This is the basic input. | ||
+ | Note that for **Task 2** and ** Task 3 ** it should be modified. | ||
<code - NaCl_gasphase.inp> | <code - NaCl_gasphase.inp> | ||
& | & | ||
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</ | </ | ||
- | ==== Motion section for constrained MD ==== | + | ==== Motion section |
- | <code - motion.inp> | + | This section has to be added to the above input file for ** Task 2 ** and ** Task 3 ** |
+ | <code - motion | ||
&MOTION | &MOTION | ||
& | & | ||
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==== Average Largange multiplier for NaCl in water at 350K (incomplete) ==== | ==== Average Largange multiplier for NaCl in water at 350K (incomplete) ==== | ||
+ | This is the Lagrange Multipliers table to be completed for ** Task 3 ** | ||
< | < | ||
# dist avg. Shake Lagrange multiplier | # dist avg. Shake Lagrange multiplier |
exercises/2015_ethz_mmm/nacl_free_energy.1426695556.txt.gz · Last modified: 2020/08/21 10:14 (external edit)