Equipment and Software
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Equiptment
My groups has access to a wide array of computational resources. Locally we have time on two High Performance Computing Cluster (HPCC) managed by OIT ( deepthought2). Time is allocated based off our allocated time from the College of Engineering. We also have acces to a joint UMD/JHU resource to perform simulations are large systems, i.e., MARCC/BlueCrab. We also have ample resources provided through XSEDE (Stampede, Comet and Bridges) and PSC/Anton2.
Back image of the Deepthought2 cluster at UMD's Riverdale Campus.
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Software
- 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.
- GROMACs: another parallel molecular dynamics program that tends to be more efficient than NAMD and compatible with the CHARMM family of FF. We also use this to run MARTINI coarse-grained simulations.
- 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 Compiling Languages: ANSI C, C++, Fortran, MPICH, JAVA, Python, etc.