This script performs several strains on a system by compressing one cell length and extending the other two cell lengths. In this way, the system is effectively stretched. After each stretch, a DPD run is performed to equilibrate the structure.

The surface tension is calculated assuming that the interface is normal to the x axis.

This can be used to study the effect of strain on the strength of an interface.

This script was inspired by a paper from Groot and Rabone[1] where they looked at stretching a lipid membrane with differing amounts of surfactant.

I have included a mesoscale template and the input molecules required to build a similar starting structure to that used by Groot and Rabone. You simply need to pack the molecules into the template using the Mesostructure Builder. You should pack the water into the "solvent" former and the lipid and surfactant into the "lipid" former. You should use a Length of 6.46 angstroms and a Density of 3.

Note that these are the same settings are used in the tutorial "Effects of surfactant on a lipid bilayer using DPD". You can find more detail on the calculation settings in that tutorial.

From a MaterialsScript perspective, this tutorial uses the new trajectory API to create the summary trajectory and uses both the new Delete and Name API on documents to delete and re-name documents. It also uses the new Stress API for reading the Stress off the trajectory.

Modules: Materials Visualizer, Mesocite
Version: 5.0

Cheers

Stephen

[1] Groot, R. D.; Rabone, K. L. Biophysical Journal. 2001, 81, 725.