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Re: Reactive polymer cross-linking

From: Peter Košovan
Subject: Re: Reactive polymer cross-linking
Date: Sun, 5 Jan 2020 23:54:52 +0100

Hi Chris,

The current reaction ensemble cannot do what you need, i.e. cross-linking polymers by creating/deleting bonds between two existing particles. We are aware of the problem. It should not be difficult to implement, but it might be tricky to make this implementation efficient in sampling the reaction equilibrium.

I do not understand your description of how you create the new monomer of type "linked". Could you send a minimalistic example script?

You cannot control the reaction volume with the current implementation. In principle, you might be able to do so, but then you would have to correct for this bias in the acceptance probability of the reaction move. Otherwise, it would break the detailed balance.

Dynamic bonds looks similar to the reaction ensemble but it simulates a different situation: bonds that are created but never destroyed anymore, i.e. an irreversible reaction. In contrast, the reaction ensemble is designed for simulating the equilibrium state of reversible reactions.

I personally think that curing and crosslinking of poly(phenylene suffide) could be described as an irreversible reaction, rather than reversible bonds that are dynamically created and destroyed. But this is presumably not an issue of espressomd.

With regards,


On Thu, Jan 2, 2020 at 10:00 PM Buurma, Chris F <address@hidden> wrote:

Hi all,

I’m new to using espresso-md, so I’ve been pouring over the documentation and examples to better familiarize myself.

I’m starting with a somewhat simple example of poly-phenylene sulfide curing and cross-linking. So I have a few polymer chains with harmonic bonds, DPD style forces, and free oxygen ‘beads’.


I setup a reaction ensemble with the reaction to take a monomer location on two different molecules along with oxygen, and then bond them. I’m currently doing this now by introducing a new monomer type ‘linked’, which I then add a new bond type after seeing its been replaced in the reaction.


Long story short: the reaction ensemble is reacting over the entire simulation space, and picking any two monomer elements, reacting them and then forcing strange long distance bonds. Can I control the reaction volume with espressomd? Ideally I’d like a small radius around the reactants.


I also looked into the cool dynamic bonds thing, but it kept creating new bonds from ‘collisions’ of my monomer elements along a polymer chain.



Chris Buurma, Ph. D.

Dr. Peter Košovan

Department of Physical and Macromolecular Chemistry
Faculty of Science, Charles University in Prague, Czech Republic

Katedra fyzikální a makromolekulární chemie
Přírodovědecká fakulta Univerzity Karlovy v Praze
Tel. +420221951029
Fax +420224919752

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