Building polymer structure

General Discussion
1

Geoffrey Hutchison <geoff@…> writes:

I’m trying to make polymer structure using Avogadro. After creating unit
cell for the monomer unit when
I try to create super cell, all the double bonds become single bonds.
Please let me know what could go wrong.
Is this the right way to create a polymer structure?

At the moment, the code does not attempt to detect multiple bonds across
unit cell boundaries. (In fact, I’d
be curious to know what polymer you’re building that has a double bond
across the repeat boundary.)

Hope that helps,
-Geoff

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I am having the same problem, but when ever I use the super cell plug in all
of the bonds are recalculated. For example I place 2 O2 molecules ( ie.
O=O O=O) in a unit cell. I then duplicate it using supercell and get O
atoms that either have a sinlge bond or no bond depending on their spacing.
All I want is for it to repeat the unit cell I created. Am I doing
something wrong?

2

Hi

I’m trying to make polymer structure using Avogadro. After creating unit
cell for the monomer unit when I try to create super cell, all the double
bonds become single bonds. Please let me know what could go wrong. Is this
the right way to create a polymer structure?

Thanks in advance.

Jyotsna

3

I’m trying to make polymer structure using Avogadro. After creating unit cell for the monomer unit when I try to create super cell, all the double bonds become single bonds. Please let me know what could go wrong. Is this the right way to create a polymer structure?

At the moment, the code does not attempt to detect multiple bonds across unit cell boundaries. (In fact, I’d be curious to know what polymer you’re building that has a double bond across the repeat boundary.)

Hope that helps,
-Geoff