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--- exercises:2015_ethz_mmm:md_ala [2015/02/06 17:49] – external edit 127.0.0.1
+++ exercises:2015_ethz_mmm:md_ala [2020/08/21 10:15] (current) – external edit 127.0.0.1
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 ====== Molecular Dynamics simulation of a small molecule======
-<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>
+<note warning>
+TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL:
-In this exercise, we will extensively use vmd for visualizing the results of the cp2k simulations.
+you@eulerX ~$ module load courses mmm vmd
-As always, give the commands:
+you@eulerX ~$ mmm-init
+</note>
-<code>
-module load cp2k/trunk.2.5.13191
+<note important> **REMEMBER: this is the command to load the  module for the cp2k program:**
-module load vmd
-mkdir EX_4.1
+<code bash>
-cd EX_4.1
+you@eulerX ~$ module load new cp2k
 </code>
-<note tip>Then, copy the ** commented ** files from the wiki: {{exercise_4.1.zip|exercise_4.1.zip}}</note>
+**and to submit the job:**
-You will start from a configuration already computed in a previous lecture, say **inp.a.pdb** which is included in the repository of this exercise as well.
+<code bash>
-Use the file **inp.nve** for the first simulation, which is a constant energy simulation.
+you@eulerX ~$ bsub < jobname
-As usual the command is **bsub cp2k.popt -i inp.nve > out.nve**
+</code>
+</note>
-  - Perform a constant energy simulation, 100000 time steps, with a time step of 1 fs.
-  - Using a different input file, modify the time step and the name of the project. Do it for 0.1, 2, 3, 4 fs.
-  - Access the corresponding *.ener files. How is the energy conservation? How is the behavior of potential and kinetic energy, and how the temperature?
-<note important>  - Plot with gnuplot the different energy conservations and discuss them.</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**
-  - Then, perform a simulation at 300 K, using the restart file from the previous simulation: **inp.300**.
-  - Now you have some outputs to study with vmd.
-The trajectory files we are going to study are
-<code>nve_md-pos-1.pdb
+Download the 4.1 exercise into your $HOME folder and unzip it:
+<code bash>
+you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_4.1.zip
+you@eulerX ~$ unzip exercises:2015_ethz_mmm:exercise_4.1.zip
+you@eulerX ~$ cd exercise_4.1
+</code>
+<note tip>
+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.
+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.
+  ???????? ???                                ! 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 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>
+  * 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 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>
+  * Have a look at the corresponding *.ener files (we suggest you to use gnuplot).
+<note tip>
+Assignments
+  - Do you see the energy conservation? Give comments on your observations.
+  - Analyse the behavior of potential and kinetic energy, and the temperature.
+</note>
+<note important>
+Hint (plotting with gnuplot).
+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>
+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>
+  * Open Tk Console (Extensions menu > Tk console). And to define the two dihedrals (**PHI** and **PSI**) from there, you can enter:
+<code tcl>
+vmd> source "dihedrals.vmd"
+</code>
-which will define the two dihedrals phi and psi.
+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.
-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.
+  * 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 important>Which differences do you notice between the nve, the 100 K and the 300 K case? Can you explain them?</note>
+<note tip>
+Which differences do you notice between the nve, the 100 K and the 300 K case? Can you explain them?
+</note>