In this exercise, we will extensively use vmd for visualizing the results of the cp2k simulations. As always, give the commands:
module load cp2k/trunk.2.5.13191 module load vmd mkdir EX_4.1 cd EX_4.1
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
The trajectory files we are going to study are
nve_md-pos-1.pdb md.100-pos-1.pdb md.300-pos-1.pdb
“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
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.