Keywords
Density Functional Theory, Molecular Dynamics, GUI
Presentation Type
Event
Research Abstract
Density Functional Theory (DFT) which is based on quantum mechanics theory has been broadly used to compute the energy and the structure of molecules and solids. However, the DFT method is limited when running calculations for a large system and only thousands of atoms can be solved. Alternatively, Molecular Dynamics (MD) simulation can be used to investigate the properties of the atomic system for large systems in the classical mechanics approximation. When running the MD simulation, the electronic structure is approximated by Force Fields (FF) which can be parametrized against DFT calculations. Nevertheless, the accuracy of the MD results and the FF is suspicious for the scientists because of the variety and complexity of the FF. Hence, a free web-browser based tool has been developed to allow the user upload a force field, run MD simulations and compare the results with the DFT calculations. Users can select desired molecules and solids in the database, run MD simulation, plot the corresponding energies and visualize the atomic structures. So that users can find out if they can trust the FF results according to the comparison with DFT calculations.
Session Track
Materials Science
Recommended Citation
Weiyi Cao, Nicolas Onofrio, and Alejandro Strachan,
"Molecular Exploration Tool"
(August 7, 2014).
The Summer Undergraduate Research Fellowship (SURF) Symposium.
Paper 63.
https://docs.lib.purdue.edu/surf/2014/presentations/63
Molecular Exploration Tool
Density Functional Theory (DFT) which is based on quantum mechanics theory has been broadly used to compute the energy and the structure of molecules and solids. However, the DFT method is limited when running calculations for a large system and only thousands of atoms can be solved. Alternatively, Molecular Dynamics (MD) simulation can be used to investigate the properties of the atomic system for large systems in the classical mechanics approximation. When running the MD simulation, the electronic structure is approximated by Force Fields (FF) which can be parametrized against DFT calculations. Nevertheless, the accuracy of the MD results and the FF is suspicious for the scientists because of the variety and complexity of the FF. Hence, a free web-browser based tool has been developed to allow the user upload a force field, run MD simulations and compare the results with the DFT calculations. Users can select desired molecules and solids in the database, run MD simulation, plot the corresponding energies and visualize the atomic structures. So that users can find out if they can trust the FF results according to the comparison with DFT calculations.
