NIH's Biowulf Cluster: A similar cluster was installed at UMD in January 2008. A high performance computational cluster was installed in January 2008. My group has contributed 24 dual quad-core Xeon Processors (E53452x4MB Cache, 2.33GHz, 1333MHz FSB) with each unit having 8GB of memory to the OIT's High Performance Computing Cluster (HPCC). This and the other units of the cluster are managed by OIT.
- CHARMM: (Chemistry at HARvard Molecular Mechanics) software package for molecular simulations of primarily biological interest. The CHARMM Development Project involves a network of developers in the United States and elsewhere working with Professor Karplus and his group at Harvard to develop and maintain the package. This program has many functions and contains the latest molecular simulation methods.
- NAMD: parallel molecular dynamics program that is extremely scalable. It can be run on hundreds of processors to efficiently characterize the dynamics of very large systems. It is compatible with coordinate and parameter files of other software such as CHARMM, AMBER, and X-PLOR. However, is limited in functionality compared to CHARMM. We typically use it to do simulations of large systems.
- Gaussian: a quantum mechanical suite of programs for ab initio calculations. Most QM methods are available in this program and is typically used to develop/improve force fields in our lab.
- VMD: (Visual Molecular Dynamics) a multiplatform molecular visualization program. It supports many different coordinate and structure file formats, including those used by CHARMM and NAMD. Most of the images and movies on this web site are created from this program.
- Various: ANSI C, C++, Fortran, MPICH, etc.
