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exercises:2015_ethz_mmm:nacl_md

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exercises:2015_ethz_mmm:nacl_md [2015/02/06 17:49] – external edit 127.0.0.1exercises:2015_ethz_mmm:nacl_md [2020/08/21 10:15] (current) – external edit 127.0.0.1
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-====== Observer NaCl dissociation ======+====== Observe NaCl dissociation ======
  
-Perform a MD simulation of NaCl in water by running the input-file ''NaCl_in_water.inp''. +This short task will help you to familiarize with Molecular Dynamics simulations. The simulation is based on forcefields, with parameters of the same type of those we used for ice (See: [[exercises:2015_ethz_mmm:monte_carlo_ice|Properties of Ice from Monte Carlo Simulations]]).
  
-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: ''NaCl_in_water.inp''.  
 + 
 +<note tip> 
 + You should run this calculation on 4 cores with ''bsub -n 4''.  
 +</note> 
 + 
 +  * 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 ''bsub -n 4''.  +
-</note>+
 ====== 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
      &COORD      &COORD
 +Na    1.0978482003279533E+01    9.1862595374996374E+00    1.3069121663365122E+01 NAP
 +Cl    1.3489457703231567E+01    1.0346547591020910E+01    1.2149103773398551E+01 CLM
 O    1.1753544421905696E+01    4.4021851582586935E+00    7.9157840505153452E+00 H2O O    1.1753544421905696E+01    4.4021851582586935E+00    7.9157840505153452E+00 H2O
 H    1.2340708249225194E+01    3.6883791978006242E+00    8.1993630993470603E+00 H2O H    1.2340708249225194E+01    3.6883791978006242E+00    8.1993630993470603E+00 H2O
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 H    1.3706746681864210E+01    3.4193537022149547E+00    2.5497917586387699E+00 H2O H    1.3706746681864210E+01    3.4193537022149547E+00    2.5497917586387699E+00 H2O
 H    1.5269466984949403E+01    3.1093971613675038E+00    2.5273427220944495E+00 H2O H    1.5269466984949403E+01    3.1093971613675038E+00    2.5273427220944495E+00 H2O
-Na    1.0978482003279533E+01    9.1862595374996374E+00    1.3069121663365122E+01 NAP 
-Cl    1.3489457703231567E+01    1.0346547591020910E+01    1.2149103773398551E+01 CLM 
      &END COORD      &END COORD
      &COLVAR      &COLVAR
        &DISTANCE        &DISTANCE
-         ATOMS 190 191+         ATOMS 1 2
        &END DISTANCE        &END DISTANCE
        &PRINT        &PRINT
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