====== 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>

In this exercise, we will extensively use vmd for visualizing the results of the cp2k simulations. 
As always, give the commands:

<code>
module load cp2k/trunk.2.5.13191
module load vmd
mkdir EX_4.1
cd EX_4.1
</code>

<note tip>Then, copy the ** commented ** files from the wiki: {{exercise_4.1.zip|exercise_4.1.zip}}</note>

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.
Use the file **inp.nve** for the first simulation, which is a constant energy simulation. 
As usual the command is **bsub cp2k.popt -i inp.nve > out.nve** 

  - 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
md.100-pos-1.pdb
md.300-pos-1.pdb
</code>

"Fire" vmd, for example **vmd nve_md-pos-1.pdb**
From the Extensions menu, you can choose the Tk console. And from there, you can enter

<code>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. 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.

<note important>Which differences do you notice between the nve, the 100 K and the 300 K case? Can you explain them?</note>