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exercises:2015_ethz_mmm:nacl_free_energy

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exercises:2015_ethz_mmm:nacl_free_energy [2015/03/18 16:19] – scleliaexercises:2015_ethz_mmm:nacl_free_energy [2015/03/18 16:21] – sclelia
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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:2015_ethz_mmm:single_point_calculation|Computation of the Lennard Jones curve]] ). \\  This case is very similar to the computation of the Lennard Jones curve (See: [[exercises:2015_ethz_mmm:single_point_calculation|Computation of the Lennard Jones curve]] ). \\ 
-  * For this you have to run the input file ''NaCl_gasphase.inp'' at a range of Na-Cl distances This can be automathized, so we provide with an template and you have to vary the MYDIST parameter in the input. +  * For this you have to run the input file ''NaCl_gasphase.inp'' at a range of Na-Cl distances. This can be automathized, so we provide with an template and you have to vary the MYDIST parameter in the input. 
   * 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 way:+  * You have to modify the input file in the following way:
     - Copy the ''NaCl_gasphase.inp'' file to a new directory and rename it to something like: ''NaCl_MD.inp''.     - Copy the ''NaCl_gasphase.inp'' file to a new directory and rename it to something like: ''NaCl_MD.inp''.
     - Change the ''RUN_TYPE''  in the new input file, from "ENERGY" to "MD".     - Change the ''RUN_TYPE''  in the new input file, from "ENERGY" to "MD".
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   * BUT take the solvated system coordinates from the previous exercise (See: [[exercises:2015_ethz_mmm:nacl_md|Observe NaCl dissociation]]). You have to copy the whole '' COORD '' section in your input.   * BUT take the solvated system coordinates from the previous exercise (See: [[exercises:2015_ethz_mmm:nacl_md|Observe NaCl dissociation]]). You have to copy the whole '' COORD '' section in your input.
   * Other slight modifications to your input:    * Other slight modifications to your input: 
-         - In the MOTION-CONSTRAINT section for a distance of 2.9 Å. +         - In the MOTION-CONSTRAINT section set TARGET to 2.9.  
          - 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**.
exercises/2015_ethz_mmm/nacl_free_energy.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1