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--- exercises:2015_ethz_mmm:md_ala [2015/03/09 15:15] – yakutovich
+++ exercises:2015_ethz_mmm:md_ala [2020/08/21 10:15] (current) – external edit 127.0.0.1
@@ Line 3: / Line 3: @@
 <note warning>
 TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:
-you@eulerX ~$ module load courses mmm vmd ; mmm-init
+you@eulerX ~$ module load courses mmm vmd
+you@eulerX ~$ mmm-init
 </note>
@@ Line 21: / Line 24: @@
-<note tip>
-Concerning temperature control, in these exercises we will use the NOSE-HOOVER chains method. This has been briefly described in the lecture, and is presented in [[doi>10.1063/1.463940|this paper]] by Glenn Martyna (1992).
-</note>
@@ Line 34: / Line 34: @@
 <note tip>
-All files of this exercise (**input and scripts are all commented**) can be also downloaded from the wiki: {{exercise_4.1.zip|exercise_4.1.zip}}</note>
+All files of this exercise (**all inputs are commented**) can be also downloaded from the wiki: {{exercise_4.1.zip|exercise_4.1.zip}}
+</note>
 You will start from a configuration already computed in the second lecture (**inp.a.pdb**) which is included in the repository of this exercise as well.
-Use the file **inp.nve** for the first simulation, which is a constant energy simulation.
+Update the following part of the file **inp.nve** for the first simulation:
 <code - md_part.inp.nve>
 &MD                                           ! This section defines the whole set of parameters needed perform an MD run.
-  ENSEMBLE NVE                                ! The ensemble/integrator that you want to use for MD propagation
+  ???????? ???                                ! Please specify the appropriete ensemble for you MD simulation
-  STEPS 100000                                ! The number of MD steps to perform
+  ????? ??????                                ! Please specify the number of MD steps to perform
-  TIMESTEP [fs] 1.0                           ! The length of an integration step
+  ???????? ???? ???                           ! Please specify the length of an integration step
-  TEMPERATURE 100.0                           ! The temperature in K used to initialize the velocities with init and pos restart velocities
+  ??????????? ?????                           ! Please specify the initial temperature
 &END MD
+</code>
+<note tip>
+To get more information, please visit **cp2k reference manual**, section **Molecular Dynamics**:
+http://manual.cp2k.org/trunk/CP2K_INPUT/MOTION/MD.html
+</note>
+  * Perform a constant energy simulation, 100000 time steps, with a time step of 1 fs. Use 100 K as an initial temperature!
+<code bash>
+you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.nve -o out.nve
 </code>
+<note tip>
+Assignments:
+  - We are performing MD at a constant energy, but why we still have to define the temperature?
+</note>
-  * Perform a constant energy simulation, 100000 time steps, with a time step of 1 fs.
+  * Make four copies of the previous input file (say inp.nve_0.1, inp.nve_2.0, inp.nve_3.0, inp.nve_4.0), in each input file modify the **time step** (use 0.1, 2, 3, 4 fs respectively)  and the **name** of the project.
+  * Perform the simulations with all these input files:
 <code bash>
-you@eulerX ~$ bsub cp2k.popt -i inp.nve -o out.nve
+you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.nve_0.1 -o out.nve_0.1
+you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.nve_2.0 -o out.nve_2.0
+you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.nve_3.0 -o out.nve_3.0
+you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.nve_4.0 -o out.nve_4.0
 </code>
-  - Using a different input file, modify the time step and the name of the project. Do it for 0.1, 2, 3, 4 fs.
+  * Have a look at the corresponding *.ener files (we suggest you to use gnuplot).
-  - Access the corresponding *.ener files. How is the energy conservation? How is the behavior of potential and kinetic energy, and how the temperature?
+<note tip>
-<note important>  - Plot with gnuplot the different energy conservations and discuss them.</note>
+Assignments
+  - Do you see the energy conservation? Give comments on your observations.
+  - Analyse the behavior of potential and kinetic energy, and the temperature.
+</note>
-  - Perform now a constant Temperature simulation. The system is in contact with a thermostat, and the conserved quantity includes the thermostat degrees of freedom. The first simulation is done at 100 K: **inp.100**
+<note important>
-  - Then, perform a simulation at 300 K, using the restart file from the previous simulation: **inp.300**.
+Hint (plotting with gnuplot).
-  - Now you have some outputs to study with vmd.
-The trajectory files we are going to study are
+To plot the Kinetic energy:
+<code bash>
+gnuplot> plot "nve_md-1.ener" u 1:3 w l t "Kinetic Energy"
+</code>
+To plot the Potential energy:
+<code bash>
+gnuplot> plot "nve_md-1.ener" u 1:5 w l t "Potential Energy"
+</code>
+To plot the Temperature:
+<code bash>
+gnuplot> plot "nve_md-1.ener" u 1:4 w l t "Temperature"
+</code>
+</note>
+Now you will perform a constant Temperature simulations, where the system is in contact with a thermostat, and the conserved quantity includes the thermostat degrees of freedom.
+<note tip>
+Concerning temperature control, in these exercises we will use the NOSE-HOOVER chains method. This has been briefly described in the lecture, and is presented in [[doi>10.1063/1.463940|this paper]] by Glenn Martyna (1992).
+</note>
+In cp2k input files you should again have a look at the following section:
+<code - md_part.inp.300>
+  &MD                                           ! This section defines the whole set of parameters needed perform an MD run.
+    ???????? ???                                ! Please specify the appropriete ensemble for you MD simulation
+    ????? ??????                                ! Please specify the number of MD steps to perform
+    ???????? ???                                ! Please specify the length of an integration step
+    ??????????? ???                             ! Please specify the temperature of the simulation
+    &??????????                                 ! Please specify a thermostat section here
+      &????                                     ! Please put here a section which specfies Nose-Hoover thermostat chain
+        TIMECON 50                              ! Timeconstant of the thermostat chain
+        LENGTH 3                                ! Length of the Nose-Hoover chain
+        YOSHIDA 3                               ! Order of the yoshida integretor used for the thermostat
+      &???
+    &???
+  &END MD
+</code>
+Edit the inp.100 file (Put there: NVT ensemble, 100000 steps of simulation, 100 K, Nose-Hoover thermostat and 1.0 fs of timestep). The first simulation is done at 100 K:
+<code bash>
+you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.100 -o out.100
+</code>
+  * Then, perform another simulation, using the restart file from the previous simulation: **inp.300**. But first you have to edit it exactly like in the previous case, but **put 300 K** instead of 100 K
+<code bash>
+you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.300 -o out.300
+</code>
-<code>nve_md-pos-1.pdb
+Now you have the following outputs to study with vmd:
+<code>
+nve_md-pos-1.pdb
 md.100-pos-1.pdb
 md.300-pos-1.pdb
 </code>
-"Fire" vmd, for example **vmd nve_md-pos-1.pdb**
+  * Open (for example) nve_md-pos-1.pdb with VMD:
-From the Extensions menu, you can choose the Tk console. And from there, you can enter
-<code>source "dihedrals.vmd"</code>
+<code bash>
+vmd nve_md-pos-1.pdb
+</code>
-which will define the two dihedrals phi and psi.
+  * Open Tk Console (Extensions menu > Tk console). And to define the two dihedrals (**PHI** and **PSI**) from there, you can enter:
-You can also pick from the extensions the "RMSD trajectory tool" and use it to align the molecule along the trajectory. Remember to replace "protein" with "all" in the selection, and then use "align". You will see that now the molecule is well aligned along the path.
-Using "Labels" menu, plot now the two dihedral angles graph.
+<code tcl>
+vmd> source "dihedrals.vmd"
+</code>
-<note important>Which differences do you notice between the nve, the 100 K and the 300 K case? Can you explain them?</note>
+You can also pick from the extensions the "RMSD trajectory tool" and use it to align the molecule along the trajectory (Extensions>Analysis>RMSC Trajectory Tool). Replace the word "protein" with "all" in the selection, and then use "align". You will see that now the molecule is well aligned along the path.
+  * Now using "Labels" menu, plot the graph of two dihedral angles:
+  - Go to Graphics > Labels
+  - In the drop-down list chose Dihedrals
+  - Chose both dihedrals in the list
+  - Go to the "Graph" section
+  - Press on the "Graph..." button
+  - (Optional) save these graps in a text file (File > Export to ASCII matrix...)
+<note tip>
+Which differences do you notice between the nve, the 100 K and the 300 K case? Can you explain them?
+</note>