The Computational Frameworks group has been setup at CRC to develop frameworks for our partner Faculty at Notre Dame. In general a framework can be considered as an abstraction, where generic codes can be specialized by the addition of user code, allowing complex (and tested) techniques to be targeted at new problems with minimal effort.
The campus has three well known Molecular simulation frameworks: Protomol, OpenMD and CASSANDRA that are supported by CI at CRC. We also develop the VisArray framework for the visualization of scientific data.
Protomol is an object-oriented, component based, framework for molecular dynamics (MD) simulations. The framework was developed by the LCLS group of Dr. Jesús Izaguirre at Notre Dame. It supports the CHARMM 19 and 28a2 force fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is designed for high flexibility, easy extendibility and maintenance, and high performance demands, including parallelization. The use of fast electrostatic force evaluation algorithms like Ewald, particle Mesh Ewald (PME), and Multigrid (MG) summation further enhances performance. Longer time steps are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover, and Langevin integrators.
OpenMD is an open source molecular dynamics engine which is capable of efficiently simulating liquids, proteins, nanoparticles, interfaces, and other complex systems using atom types with orientational degrees of freedom (e.g. “sticky” atoms, point dipoles, and coarse-grained assemblies). Proteins, zeolites, lipids, transition metals (bulk, flat interfaces, and nanoparticles) have all been simulated using force fields included with the code. OpenMD works on parallel computers using the Message Passing Interface (MPI), and comes with a number of analysis and utility programs that are easy to use and modify. An OpenMD simulation is specified using a very simple meta-data language that is easy to learn.
Cassandra is a Monte Carlo molecular modeling software that is designed in Fortran 90 following a modular philosophy with the ultimate goal of open source development. The code is being developed keeping in mind flexibility, high performance, ease of extensibility and ability to handle a large number of molecular systems ranging from a simple Lennard-Jones particles to large protein systems. It offers parallelization with openMP to take advantage of multicore processing capabilities of today's hardware.
VisArray is a visualization framework for rendering scientific data. By combining data acquisition and manipulation in front-end modules with flexible back-end rendering modules our framework has been targeted at a diverse range of projects, from clustering of social network data to visualizing fibrin networks formed during thrombus development. The resulting display can be rendered to traditional displays, 3D hardware, ray traced, embedded in web-portals and, more recently, projected onto the Digital Visualization Theater (DVT) facility at Notre Dame's Jordan Hall of Science.