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exercises:2017_uzh_acpc2:l-j_flu [2017/04/24 10:35] – [Background] jglanexercises:2017_uzh_acpc2:l-j_flu [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 <note>**TASK** <note>**TASK**
   *Run the calculation and visualize the trajectories using VMD   *Run the calculation and visualize the trajectories using VMD
-  *Run calculations with different timesteps (0.5 2 5fs), different temperatures(84, 300, 400K), different densities($\rho$=0.25,0.5,1), and a different number of timesteps (100,1000,5000), and inspect geometry in each case.+  *Run calculations with different timesteps (0.5 2 5fs), different temperatures(84, 300, 400K), different densities($\rho$=0.25,0.5,1), and a different number of timesteps (100,1000,5000), and inspect geometry in each case, plot the total energies, temperature, potential energies. Try to comment and explain what you observe.
 </note> </note>
 ===== Part II:  Force Field Parameter  ===== ===== Part II:  Force Field Parameter  =====
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 Step up NPT calculation, change the setting in &MD section.   Step up NPT calculation, change the setting in &MD section.  
  
 +  &FORCE_EVAL
 +  ...
 +  STRESS_TENSOR ANALYTICAL
 +  ...
 +  &END FORCE_EVAL
 +  ...
 +  ...
   &MD   &MD
     ENSEMBLE NPT_I                #constant temperature and pressure using an isotropic cell     ENSEMBLE NPT_I                #constant temperature and pressure using an isotropic cell
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         TIMECON 1000         TIMECON 1000
       &END NOSE       &END NOSE
 +   &END MD
  
 <note> <note>
exercises/2017_uzh_acpc2/l-j_flu.1493030154.txt.gz · Last modified: 2020/08/21 10:15 (external edit)