CP2K Open Source Molecular Dynamics

User Tools

Site Tools

Trace:
exercises:2015_ethz_mmm:nacl_free_energy

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
Last revisionBoth sides next revision
exercises:2015_ethz_mmm:nacl_free_energy [2015/03/18 16:19] – scleliaexercises:2015_ethz_mmm:nacl_free_energy [2015/03/18 16:48] – [3. Task: Free energy curve of NaCl in water at 350K] sclelia
Line 12: Line 12:
 ===== 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.
  
Line 18: Line 18:
  
 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".
Line 64: Line 64:
  
   * 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**.
Line 78: Line 78:
  
 ==== 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
Line 156: Line 157:
 </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
Line 205: Line 207:
  
 ==== 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
exercises/2015_ethz_mmm/nacl_free_energy.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1