An Implementation of a Graphical Interface for Molecular Simulation Software using Python and Qt4

Abstract

Molecular Dynamics (MD) is being used for simulating prototypes of nanodevice components that combine CNT, graphene and/or polymers. However, there are plenty of difficulties with creating a system for simulations, especially if it has many different molecules or if you need to create the coordinate, topology and configuration files from scratch. Wolffia has been developed as a tool that integrates diverse MD software to guide the user throughout the simulation process. The design of the software was done as follows. Based on input from scientists with experience modeling using MD the different steps of the process were outlined. The programming language that was selected, Python, facilitated portability and access to libraries needed for the representation of molecule systems. Libraries for such representation were chosen taking into consideration their usability for the study of structure analysis and for statistical physics. Python, the chosen graphical user interface (GUI) library, provided the best programming tools possible and with a variety of widget libraries available. The resulting main GUI consists of five tabs corresponding to the steps required for the simulation process: build, setup, minimization, simulation, and analysis of trajectories. The GUI was implemented using the PyQt4 libraries that allow the programmer to use the sophisticated Qt Designer software and give access to many third party widget libraries. Among the widget libraries evaluated, the PyQt4, PyOpenGl, Qwt contain the most appropriate collections of widgets for this application. New widgets were developed by specializing classes from these collections. For example, selections of predefined molecules using a subclass of QTreeWidget. A mixture preview widget was built instantiating the QtOpenGL class. Moving plots for tracking physical measurements of the simulated systems are visualized with a subclass of QwtPlotCurve from the Qwt5 library. These widget collections have been combined and specialized successfully, resulting in Wolffia, an integrated application for performing MD simulations, which facilitates user-software interaction. This user-friendly tool has been proved to be effective to easily setup CNT-Polymer composites.