Software and Resources

The parallel computing lab utilizes several resources, software, and tools for the purpose of simulating membranes.

Rocks Linux distribution. All of the clusters benefit from this open-source platform. It includes many built-in capabilities to make a clusters easier to install, use, and manage.

OpenMPI parallel libraries. This open-souce implementation of the Message Passing Interface supports the diversity of hardware and network switches present in the lab.

Anton supercomputer at PSC. Dr. Feller was granted some computing time on this supercomputer, capable of microsecond simulations, that was designed for biomolecular simulation from the ground up. The molecular modeling implementation is based on Desmond software.

CHARMM-GUI. This web resource offers a guided procedure to build and prepare virtual membranes, supporting CHARMM and NAMD formats. It allows both students and seasoned users to quickly start a simulation.

CHARMM. As a contributer to CHARMM source code, Dr. Feller uses this MD simulation software as the primary means for modeling bilayers. The flexibility in the large suite of included tools allows for greater control over simulation conditions. CHARMM also provides extensive analysis capabilities. A community supported mailing list is good at providing helpful advice.

NAMD. NAMD is a free software package designed for molecular dynamic simulations of biological molecules. With a few caveats, simulation files are compatible with CHARMM formats. With standard CUDA support, the lab uses NAMD to run simulations on the GPU-accelerated workstation.

Spartan. Spartan is a molecular modeling and analysis program used in classrooms and the lab. Spartan allows the user to build molecules in a graphical environment, and to manipulate and analyze them using empirical or quantum mechanical functions.

VMD. This provides a high quality visual guide to the atomic coordinates in a simulation. It is capable of making photo-realistic renderings for figures.

Gnuplot. This is a free, command-line driven, and very handy graphing utility.

The lab also makes use of various analysis code developed by Matt Roark, with descriptions available in the Analysis section of the Wabash Computing Guide.

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