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exercises:2017_uzh_acpc2:mol_sol [2017/05/04 14:40] – [Water] jglanexercises:2017_uzh_acpc2:mol_sol [2020/08/21 10:15] (current) – external edit 127.0.0.1
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-====== Potential energy surface of glyala dipeptide ======+====== Molecular Solution ======
  
 ===== Ramachandran plot ===== ===== Ramachandran plot =====
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 In particular, it has more than one long-lived conformation, which we will identify in this exercise by mapping out its //potential energy surface//. In particular, it has more than one long-lived conformation, which we will identify in this exercise by mapping out its //potential energy surface//.
  
-The conformations of alanine dipeptide are characterized by the dihedral angles of the backbone.+The conformations of glyala dipeptide are characterized by the dihedral angles of the backbone.
 Below, we color carbons in green, hydrogens in white, oxygen in red and nitrogen in blue, i.e.  Below, we color carbons in green, hydrogens in white, oxygen in red and nitrogen in blue, i.e. 
 the torsional angle $\phi$ is N-C-C-N , while $\psi$ is C-N-C-C along the backbone. the torsional angle $\phi$ is N-C-C-N , while $\psi$ is C-N-C-C along the backbone.
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   - The atomic indices defining the dihedral indices in the input file ''geo.in'' are missing. Replace ''I1'' to ''I4'' by the atomic indices determined previously. //Note:// While VMD starts counting atoms from 0, CP2K starts counting from 1, i.e. the VMD indices need to be increased by 1.   - The atomic indices defining the dihedral indices in the input file ''geo.in'' are missing. Replace ''I1'' to ''I4'' by the atomic indices determined previously. //Note:// While VMD starts counting atoms from 0, CP2K starts counting from 1, i.e. the VMD indices need to be increased by 1.
   - Use ''perform-gopt.sh'' to perform the grid of geometry optimizations.   - Use ''perform-gopt.sh'' to perform the grid of geometry optimizations.
-  - Use gnuplot to plot the potential energy surface (we have provided a script ''epot.gp''). Which are the two most favoured conformations? <code> $ gnuplot</code><code> gnuplot >> load "epot.gp"</code>+  - Use gnuplot to plot the potential energy surface (we have provided a script ''epot.gp''). Which are the two most favoured conformations? <code> $ gnuplot</code><code> gnuplot > load "epot.gp"</code>
 </note> </note>
 ===== Water ===== ===== Water =====
-We have prepared a CP2K input file ''md.in'' for running a MD simulation of liquid water using the force field from the first exercise (parametrized by Praprotnik et al.).+We have prepared a CP2K input file ''water.inp'' for running a MD simulation of liquid water using the force field from the first exercise (parametrized by Praprotnik et al.). Download {{water.tar.gz}}
  
-<note>**TASK 1**+Repeat the MD using initial temperatures 200 and 400 K. In order not to overwrite any of your previous files, it is advisable to run the new simulations in different folders.
  
 +<note>**TASK 3**
   * Check that the MD is energy conserving and //well-behaved//   * Check that the MD is energy conserving and //well-behaved//
-</note> +  * What are the final average temperatures in each of the simulations? Why are they different from the initial ones?
- +
- +
-Repeat the MD using initial temperatures 200 and 400 K. In order not to overwrite any of your previous files, it is advisable to run the new simulations in different folders. +
- +
-<note>**TASK 2** +
- +
-  * What are the final average temperatures in each of the simulations? +
-  * Why are they different from the initial ones?+
   * The initial atomic configuration stems from an equilibration run. At which temperature was the system (approximately) equilibrated?   * The initial atomic configuration stems from an equilibration run. At which temperature was the system (approximately) equilibrated?
 </note> </note>
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 VMD comes with an extension for exactly this purpose: In the VMD Main window open "Extensions -> Analysis" click on "Radial Pair Distribution function $g(r)$". In the appearing window use "Utilities -> Set unit cell dimensions" to let VMD know the simulation box you used. After that use Selection 1 and 2 to define the atomic types that you want to calculate the rdf for, for example "element H". VMD comes with an extension for exactly this purpose: In the VMD Main window open "Extensions -> Analysis" click on "Radial Pair Distribution function $g(r)$". In the appearing window use "Utilities -> Set unit cell dimensions" to let VMD know the simulation box you used. After that use Selection 1 and 2 to define the atomic types that you want to calculate the rdf for, for example "element H".
  
-<note>**TASK 3**+<note>**TASK 4**
  
   * Plot $g_{O-O}(r)$ at 200, 300 and 400 K into the same graph.   * Plot $g_{O-O}(r)$ at 200, 300 and 400 K into the same graph.
   * What are the differences in the height of the first peak?   * What are the differences in the height of the first peak?
-  * What does this say about the structure of the liquid and is this expected? (2P)+  * What does this say about the structure of the liquid and is this expected? 
   * Compare to experimental data ''goo.ALS'' taken at 300 K.    * Compare to experimental data ''goo.ALS'' taken at 300 K. 
 </note> </note>
  
-Then we will calculate diffusion coefficient.+Then we will calculate diffusion coefficient. It is a proportionality constant between the molar flux due to molecular diffusion and the gradient in the concentration of the species (or the driving force for diffusion), which is defined by: 
 +**$6D=\lim_{t\to\infty}  \ \frac{\delta <r^2(t)>}{\delta t}$**
  
-The diffusion  coefficient is a proportionality constant between the molar flux due to molecular diffusion and the gradient in the concentration of the species (or the driving force for diffusion), which is defined by: 
-**$6D=\lim_{t\to\infty}  \ \frac{\delta <r^2(t)>}{\delta t}$** 
 To evaluate this expression, all that is needed is to evaluate at each point in time in the calculation the average of the square of the distance that each atom has traveled since the start of the production phase of the dynamics, and examining the slope of this function at a long time. By storing the initial coordinates, it is straightforward to evaluate the square of the distance. However, some care is needed due to the use of periodic boundary conditions: the program stores x, the coordinates, but in many programs, during the dynamics, if any atom has its x, y, or z coordinate become larger than box size or smaller than zero, then it is moved back into the other side of the box. This has the effect of making the raw distance traveled meaningless. The value of D is obtained from the slope, at a long time, of the right-hand side of the above equation (you need to divide by six to obtain D, take the slope, and also be careful with units). To evaluate this expression, all that is needed is to evaluate at each point in time in the calculation the average of the square of the distance that each atom has traveled since the start of the production phase of the dynamics, and examining the slope of this function at a long time. By storing the initial coordinates, it is straightforward to evaluate the square of the distance. However, some care is needed due to the use of periodic boundary conditions: the program stores x, the coordinates, but in many programs, during the dynamics, if any atom has its x, y, or z coordinate become larger than box size or smaller than zero, then it is moved back into the other side of the box. This has the effect of making the raw distance traveled meaningless. The value of D is obtained from the slope, at a long time, of the right-hand side of the above equation (you need to divide by six to obtain D, take the slope, and also be careful with units).
 +
 +VMD comes with an extension for exactly this purpose: In the VMD Main window open “Extensions → Analysis” click on “RMSD Trajectory Tool”. In the appearing window use “all” to let VMD know the molecule you want to track. Tick "Plot", and press "RMSD", you will have the RMSD plot for the water system.
 +
 +<note>**TASK 5**
 +  * Plot RMSD for the water at 200K, 300K, 400K.
 +  * Calculate their corresponding diffusion coefficients, are they expected?
 +</note>
 ===== Glyala in water ===== ===== Glyala in water =====
 Now, we will move to a more realistic system - Glyala in water. We will preformed a MD of glyala in water and save the trajectory. Now, we will move to a more realistic system - Glyala in water. We will preformed a MD of glyala in water and save the trajectory.
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-<note>**TASK 3**+<note>**TASK 6**
    - Perform the molecular dynamics simulation using NVT ensemble at 300K.    - Perform the molecular dynamics simulation using NVT ensemble at 300K.
    - Re-run the calculation using NVT ensemble with different TIMECON (500, 2000 fs) in the &THERMOSTAT section, and plot the total energy, temperature against time. Explain what you observe.    - Re-run the calculation using NVT ensemble with different TIMECON (500, 2000 fs) in the &THERMOSTAT section, and plot the total energy, temperature against time. Explain what you observe.
exercises/2017_uzh_acpc2/mol_sol.1493908812.txt.gz · Last modified: 2020/08/21 10:15 (external edit)