VCMM: A visual tool for continuum molecular modeling

• VCMM provides the tools to facilitate the whole simulation processes, such as force field tools, mesh generation tools, mesh analysis tools and numerical solvers.
• VCMM will enhance the capability of molecular visualization tools to handle unstructured mesh which is wildly used in boundary and finite element methods.
• We develop a variety of novel and practical visualization methods.

This paper describes the design and function of a visualization tool, VCMM, for visualizing and analyzing data, and interfacing solvers for generic continuum molecular modeling. In particular, an emphasis of the program is to treat the data set based on unstructured mesh as used in finite/boundary element simulations, which largely enhances the capabilities of current visualization tools in this area that only support structured mesh. VCMM is segmented into molecular, meshing and numerical modules. The capabilities of molecular module include molecular visualization and force field assignment. Meshing module contains mesh generation, analysis and visualization tools. Numerical module currently provides a few finite/boundary element solvers of continuum molecular modeling, and contains several common visualization tools for the numerical result such as line and plane interpolations, surface probing, volume rendering and stream rendering. Three modules can exchange data with each other and carry out a complete process of modeling. Interfaces are also designed in order to facilitate usage of other mesh generation tools and numerical solvers. We develop a technique to accelerate data retrieval and have combined many graphical techniques in visualization. VCMM is highly extensible, and users can obtain more powerful functions by introducing relevant plug-ins. VCMM can also be useful in other fields such as computational quantum chemistry, image processing, and material science.

A tetrahedral mesh of an ion channel system. The membrane and the protein region are shown in red, solvent reservoirs and the channel region are shown in transparent navy blue.Figure optionsDownload high-quality image (180 K)Download as PowerPoint slide