Generate Dimer / Trimer / Tetramer

[nandass]

Sir , could you please tell me on how to generate a dimer/trimer/tetramer of a molecule in avogadro?

[ghutchis]

It would help to know what you mean by dimer / trimer / tetramer.

Do you mean “take this repeat unit and generate an oligomer with covalent bonds”?

Or do you mean “I want two molecules separated by 5 A”?

[nandass]

sir
it is to create a dimer/tetramer with same molecule through covalent bonds.

[ghutchis]

Edit => Copy
Edit => Paste

Move into approximately the position you want

Draw the bond you want between the atoms = you have a dimer

From dimer to tetramer, you repeat the process:

Edit => Copy … now the dimer
Edit => Paste … now you have four copies of your original monomer

Move into place, and draw the bond connecting the two dimers

Optimize the geometry:

[nandass]

Thankyou so much sir.
would also like to ask one more question ; can we generate a PTFE surface in avogadro?

[nandass]

sir
sorry to ask it one more time
can you also say about the method adopted to keep molecules at a distnce of 5/4 angstrom?

[ghutchis]

Well, in that case, e.g. in Avo1.2, you copy the molecule, paste the molecule.

Now the manipulate tool is chosen, and you can move the pasted (selected) molecule as you want:

So, for example, you can put in 5 A on the x-axis and click “Apply”

Repeat as you wish.

[nandass]

thankyou sir.
Can we have metal ions inserted through avogadro?like Na+

[ghutchis]

Happy to help - can you please start new topics if you have more questions? This makes it easier for others to find if they have similar questions. Thanks!