force-bdss-plugin-surfactant-example

Example plugin for example surfactant formulation use-case. Requires a force-bdss installation, including the force-bdss-plugin-gromacs wrapper.

Additional modules that can contribute to the force-wfmanager UI are also included, but a local version of force-wfmanager is not required in order to complete the installation.

Installation Instructions

To install force-bdss and the force-wfmanager, please see the following instructions.

To install the force-bdss-plugin-gromacs package, please see the following instructions

Afterwards, clone the git repository

git clone https://github.com/force-h2020/force-bdss-plugin-surfactant-example.git

After downloading, enter the source directory and run:

python -m ci install

This will allow install the plugin in the force-py36 edm environment, allowing the contributed BDSS objects to be visible by both force-bdss and force-wfmanager applications.

Plugin Functionality

This plugin takes in user input for a simulated experiment to be run using Gromacs molecular dynamics engine. The MCO parameters refer to concentrations of Surfactant and Salt chemical species. There are 3 different parameter types:

• FixedMCOParameter: A parameter defining a fixed concentration
• RangedMCOParameter: A parameter defining a range of concentrations between a lower and upper bound
• ListedMCOParameter: A parameter defining a list of concentrations that have been inputted by the user

A typical set up contains 4 sequential layers containing with the following models:

1. Fragment: A Gromacs simulation is comprised of multiple molecular fragments, representing a molecular species connected by covalent bonds. These fragments may be single or multiple particles and may or may not be charged. Initally they must be defined and imported using the force-bdss-plugin-gromacs wrapper.

2. Ingredient: An Ingredient object represents a set of Fragments that form a neutral molecular species and can be assigned real-world attributes such as concentration and price. There are 3 different ingredient roles: Surfactant, Salt and Solvent, for which at least one Ingredient must be assigned to in any simulation (note: at the moment, the plugin only supports one solvent Ingredient per simulation). Additionally, any non-solvent Ingredients must also be assigned a concentration, which can be inputted as an MCOParameter.

3. Simulation: Each different Simulation takes in a set of chemical Ingredients and MD parameters. A script to run a Gromacs MD simulation is then generated and ran locally if desired, or can be piped into a HPCWriter for preparation to be submitter to a remote cluster.

4. Cost + Micelle: This layer calctlates the KPIs required for the surfactant formulation use case: material cost and micelle aggregation number. The Micelle calculator is expected to perform post-processing operations on the simulation output in order to estimate the average micelle aggregation number of the mixture. Similarly, the Cost calculator is able to generate an estimate of material costs, proportional to the price and concentration of each ingredient.

ContributedUI Functionality

A simplified UI is supplied for non-technical users. This allows for selection of a primary surfactant and (optional) secondary surfactant, as well as both the range of surfactant and salt concentrations to investigate.

The UI will then create Gromacs scripts to run a range of MD simulations using NaCl as the salt ingredient and water as a solvent.