Solution LAB2 guanine

• Back to the previous page: Electronic properties of isolated molecules#Exercise1

Step 1

• Once you have Avogadro installed, open it and let's use the molecular builder to visualise a Guanine molecule:

Build --> Insert-->Fragment-->nucleobases-->guanine

Click on the selection settings "arrow" and right click to visualise the molecule.

Clicking on manipulate settings "hand" you can then rotate the molecule.

• Now we perform a classical relaxation using an Avogadro built-in Force Filed

Extension-->Molecular Mechanics and we choose a FF

Extension-->Optimize geometry

In few steps we have our relaxed geometry that we can save in .xyz format using:

File-->Save as-->select .xyz format and save in your disk as guanine_FF.xyz

Step 2

Now we are ready to perform a QM relaxation. As a first step, update your pseudo potentials directory by using git commands:

git pull

new pseudo potentials (Nitrogen and Oxygen) will be downloaded in your pseudo potential directory.

Create a relax input paying attention to:

forc_conv_thr = 1.0d-3 #we set a low threshold in order to not have a too long calculation 
ibrav=8 #orthorombic cell with vacuum
celldm(1) = 25.00
celldm(2) =  1.0
celldm(3) =  0.8

Set the correct number and types of atoms. Set all the atomic species using the psuedo you have downloaded:

H   1.0  H.pz-vbc.UPF
C   1.0  C.pz-vbc.UPF
N   1.0  N.pz-vbc.UPF
O   1.0  O.pz-mt.UPF

insert the atomic positions in Angstrom:

ATOMIC_POSITIONS (angstrom)

Important: How many k points you need?

Run the relaxation, it will take a while to rearrange the atoms in the relaxed positions according to the threshold parameter. One the job has converged you can compare the initial position (Force Field relaxed) with the final ones (QM relaxed). You can use xcrysden to visualise the optimisation steps.

 xcrysden --pwo guanine_relax.out

you can reduce the dimensionality to 0D and choose the option: Display All Coordinates as Animation In this way you will have a movie of the molecule relaxation