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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 [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: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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   * 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:2015_ethz_mmm:nacl_md|Observe NaCl dissociation]]). You have to copy the whole '' COORD '' section in your input.+  * BUT take the forcefield and the solvated system coordinates from the previous exercise (See: [[exercises:2015_ethz_mmm:nacl_md|Observe NaCl dissociation]]). In practice, you have to substitue the whole '' FORCE EVAL '' section in the ** Task 2** input with the '' FORCE EVAL '' section of [[exercises:2015_ethz_mmm:nacl_md|Observe NaCl dissociation]].
   * 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**.
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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>
 &FORCE_EVAL &FORCE_EVAL
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 </code> </code>
  
-==== Motion section for constrained MD ==== +==== Motion section TO ADD for constrained MD ==== 
-<code - motion.inp>+This section has to be added to the above input file for ** Task 2 ** and ** Task 3 ** 
 +<code - motion section>
 &MOTION &MOTION
  &CONSTRAINT  &CONSTRAINT
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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 **
 <code> <code>
 # dist     avg. Shake Lagrange multiplier # dist     avg. Shake Lagrange multiplier
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