In this tutorial you will learn how to build polymers from monomers using the polymer builder tool of AMS.
As an example polymer we are going to build high-impact polystyrene (HIPS), a low cost thermoplastic that is easy to fabricate and often used for low strength structural applications where impact resistance and machinability are required. HIPS is a graft polymer consisting of a polystyrene backbone with polybutadiene chains branching from it in each direction.
Loading the monomers from the database¶
In principle we could build the monomers ourselves using the normal building tools and the molecule viewport on the left. We would then also have to designate the link points at which the monomers can link up. However, in practice it is easier to just load them from the monomer database that comes with the Amsterdam Modeling Suite.
You should now see the two monomers in the molecule viewport.
Note that each of the two monomers has two link points, designated by the small light blue spheres and the label, e.g.
1A. The number in the label designates the monomer that this link point belongs to (in the order they were loaded/built), while the letter labels the different link points on each monomer.
Let us first set up the polystyrene back bone. We would obtain pure polystyrene if we just linked the styrene monomers via
1A ↔ 1B. Let us actually do that now.
As you can see, we now have a pure polystyrene chain, while the butadiene monomer was not used at all. This is simply because we did not set up a linking rule that included any of its link points. Let us fix this now and grow real high-impact polystyrene.
In order to attach polybutadiene side chains to the polystyrene backbone, we first need to add more link points to the styrene monomer. Otherwise there is just no place to attach the side chains without terminating the backbone.
1A link. (Shift + left click adds atoms to a selection.)
The last carbon atom in the tail of the styrene monomer should now have three link points. We already used
1A to make backbone link to
1B. Ergo we can not use this link to attach the butadiene chains since it might terminate our backbone. However, we can use the newly created links
1D to grow the side chains.
This allows the attachment of butadiene monomers to our backbone. However, we also want these side chains to be able to grow into polybutadiene. Ergo we need to set up one last link, which allows linking of the butadiene monomers to each other.
The polymer builder grows the polymers by randomly making the links according to the weight we have set for each link. As our backbone grows we get more and more open ended side chains, to which more butadiene monomers could be linked. On the other hand, the number of link points at which the backbone can be grown is constant: one at each end of the backbone chain! Randomly picking new links with equal weights would therefore lead to a very short backbone with extremely long side chains, which is probably not what we want. We will therefore decrease the weight of the link between butadiene monomers in order to control the length of the side chains.
This is all we need. We are now ready to start growing the high-impact polystyrene polymer.
As the polymer is growing you can see the labels of the currently still open link points. As mentioned above these are mostly the open
2B link points, hence the lower weight for the
Optimizing the structure with UFF¶
Once the entire polymer has been built, we should optimize its geometry with UFF. The polymer builder is relatively aggressive in linking together the monomers, and while it will make sure the result is sterically not completely unreasonable, it might still have groups from different monomers unphysically close to each other. A quick optimization with UFF is perfect to resolve these situations, as it will use the topology set up by the polymer builder and not form or break bonds during the optimization. The UFF forcefield is the default forcefield in the ForceField module.
Always optimize the output of the polymer builder with UFF. As of AMS2020, the UFF forcefield is now part of the ForceField module.
You will probably see the energy decrease a lot in the first few optimization steps where UFF resolves all the steric conflicts. Once the optimization is complete you should have a beautiful polymer:
In practice you may also want to build periodic boxes full of (cross-linked) polymers. Building these is harder, but can be done with biased molecular dynamics calculations using reactive force fields, see the tutorial:
Alternatively, one can pack a simulation box with polymer molecules and equilibrate them:
More tutorials on mechanical properties of polymers can be found here: