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exercises:2017_uzh_acpc2:l-j_flu [2017/04/24 10:30] – [Background] jglanexercises:2017_uzh_acpc2:l-j_flu [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 where is $\epsilon$ the well depth, σ is related to the minimum of Lennard-Jones potential, rij is the where is $\epsilon$ the well depth, σ is related to the minimum of Lennard-Jones potential, rij is the
 distance between atoms i and j. distance between atoms i and j.
-[[https://en.wikipedia.org/wiki/Periodic_boundary_conditions/|Periodic boundary conditions]]should be used in this simulation. The atom near the ”edge” + 
-of the simulation box interacts with atoms contained in the neighboring image of the box. To +[[https://en.wikipedia.org/wiki/Periodic_boundary_conditions|Periodic boundary conditions]] should be used in this simulation. The atom near the ”edge” of the simulation box interacts with atoms contained in the neighboring image of the box. In computer simulations, one of these is the original simulation box, and others are copies called images. During the simulation, only the properties of the original simulation box need to be recorded and propagated. The minimum-image convention is a common form of PBC particle bookkeeping in which each individual particle in the simulation interacts with the closest image of the remaining particles in the system. To prevent artifacts, it requires a cut-off value of rij for the L-J potential. For realistic results, the cut-off should be less than the half of the simulation box size and over σ Radial distribution
-prevent artifacts, it requires a cut-off value of rij for the L-J potential. For realistic results, the +
-cut-off should be less than the half of the simulation box size and over σ Radial distribution+
 function, (or pair correlation function) $g(r)$ in a system of particles (atoms, molecules, colloids, function, (or pair correlation function) $g(r)$ in a system of particles (atoms, molecules, colloids,
 etc.), describes how density varies as a function of distance from a reference particle. etc.), describes how density varies as a function of distance from a reference particle.
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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>
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