Sir , could you please tell me on how to generate a dimer/trimer/tetramer of a molecule in avogadro?
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”?
it is to create a dimer/tetramer with same molecule through covalent bonds.
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:
Thankyou so much sir.
would also like to ask one more question ; can we generate a PTFE surface in avogadro?
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?
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.
Can we have metal ions inserted through avogadro?like Na+
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!