Computing

Computational work in our group requires the use of high performance hardware and software.

Our main computational tool is 3D-RISM, which is distributed with the AmberTools molecular modeling suite and is capable of running on large computational clusters across multiple nodes. Calculations run on our local cluster, as well as national resources, such as XSEDE. We continue to improve the performance of 3D-RISM by using numerical methods, such as treecode summation and multigrid solvers.

Students in our group work in a Linux environment and use software such as BASH, Python, Torque/Maui, Slurm, MPI, and Emacs on a daily basis. In addition to running – and sometimes coding – simulations, students also analyze data sets with millions of entries.