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Expanding the MoSDeF framework

Primary Investigators:
Clare McCabe
 
Brief Description of Project:
The MoSDeF framework (https://mosdef.org) is a set of open-source Python libraries designed to accelerate molecular simulation by automating each of the steps in a workflow. For most projects, these steps include: determining the desired physiochemical inputs, specifying the configuration of a molecular system, determining and applying the proper physics-based model to the system, and sending this information to a simulation engine through scripts. In some projects, it is also beneficial to screen over many systems rapidly to glean insights over large physiochemical space.

The goal of this summer research is to increase MoSDeF’s support for a particular molecular model, the Optimized Potential for Liquid Simulations - all atom (OPLS-AA) force field, and validate its implementation in MoSDeF through molecular simulations. The student will work with a graduate student to develop the chemical systems to validate, better encode OPLS-AA into MoSDeF, and run simulations to perform the validation. Comparisons will be made between the output of this MoSDeF/OPLS-AA simulations, reference simulation data in literature, and tabulated physical properties from experiments.

By the end of the summer, the student should have sufficient knowledge of molecular simulation, as well as the ability to work with different software to prepare and run molecular simulations. Along the way, the student will gain experience working with modern Python libraries in the scope of larger workflows with other components.

Desired Qualifications:
Interest in computational research, some experience with python or similar programming language
 
Nature of Supervision:
The undergraduate student will work closely with a graduate student and the larger MoSDEF group.
 
A Brief Research Plan (period is for 10 weeks):
Week 1: Onboarding
Tutorial: Linux command prompt, Github, Python
Tutorial: Molecular Simulation
Learn about MoSDeF (mbuild and foyer)
Understanding why SMARTS strings matter
Introduction to popular simulation engines

Week 2 - 8: Obtaining data
Preparing systems:
Collecting reference data and determining which systems to run
Filling missing SMARTS entries to foyer XML file
Running simulations with different engines:
Doing engine-specific tutorials
Preparing scripts to run the simulations for different engines
Running the simulation and analyzing data (extracting physiochemical properties, such as bulk density, heat capacity, and compressibility)

Week 9 - 10: Wrapping up
Comparing the data obtained from different simulation engines, and compare those with the original papers.
Preparing the poster 

Number of Open Slots: 2
 
Contact Information:
Name: Clare McCabe
Department: Chemical and Biomolecular Engineering
Email: c.mccabe@vanderbilt.edu