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--- exercises:2015_ethz_mmm:md_ala [2015/03/09 16:18] – 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}}
+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>
-  * Perform a constant energy simulation, 100000 time steps, with a time step of 1 fs.
+<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>
-  * Using a different input file, modify the time step and the name of the project. Do it for 0.1, 2, 3, 4 fs.
+<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.
-  - Describe the behavior of potential and kinetic energy, and the temperature.
+  - Analyse the behavior of potential and kinetic energy, and the temperature.
 </note>
@@ Line 80: / Line 99: @@
 </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. In cp2k input file it can be specified as follows:
+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.
-    ENSEMBLE NVT                                ! 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 1.0                                ! The length of an integration step
+    ???????? ???                                ! Please specify the length of an integration step
-    TEMPERATURE 300.0                           ! The temperature in K used to initialize the velocities with init and pos restart velocities
+    ??????????? ???                             ! Please specify the temperature of the simulation
-    &THERMOSTAT                                 ! This section specifies thermostat type and parameters controlling the thermostat
+    &??????????                                 ! Please specify a thermostat section here
-      &NOSE                                     ! This section specifies paramameters of the Nose Hoover thermostat chain
+      &????                                     ! Please put here a section which specfies Nose-Hoover thermostat chain
         TIMECON 50                              ! Timeconstant of the thermostat chain
-      &END NOSE
+        LENGTH 3                                ! Length of the Nose-Hoover chain
-    &END
+        YOSHIDA 3                               ! Order of the yoshida integretor used for the thermostat
+      &???
+    &???
   &END MD
 </code>
-The first simulation is done at 100 K:
+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 a simulation at 300 K, using the restart file from the previous simulation: **inp.300**.
+  * 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
@@ Line 120: / Line 147: @@
 <code tcl>
-source "dihedrals.vmd"
+vmd> source "dihedrals.vmd"
 </code>
 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.
+  * 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>