Hi there,

I am pleased to post the first version of the network building script for atomistic models of polymers. This follows on from the mesoscale cross-linking script that I posted earlier this year (in fact, most of the initial work was just search and replace through that script).

This script was written as part of the Nanointerface EU project and hence it focuses on building networks for epoxy oligomers with a cross-linking molecule. In the example structure, the cross-linker is bisphenol-A and the oligomer is a Novolac type polymer. The script includes a specific function to open the epoxy ring as it “reacts” hence the input Novolac oligomer has closed epoxy rings. The ring opening can be disabled so that the script can also be used for any system where you have two different “reactive” atoms on different molecules.

The script uses the same method as outlined for the mesoscale cross-linking script so I won’t go through it all again. However, there have been some changes:

• Moved a short geometry optimization run straight after the connections have been created
• Added geometry optimization calculations at the end of both the temperature cycle and straight dynamics subroutines
• Close contact list is randomized
• Added ring-opening option (only works for epoxies)
• Hydrogens are adjusted after connections are created to re-adjust valences
• Improved handling of intermediate trajectory file names
• Cross-link statistics aren’t calculated if no bonds are added (cleaner text output)
• All text info is written to “progress.txt” which can be viewed on the server

Limitations:

• No checking for ring spearing when bonds are created
• Intramolecular bonds can be formed if R1 and R2 are on the same molecule
• Each molecule must have at least two atoms marked R1 or R2.
• This is still an experimental script!

Have fun.

Cheers

Stephen