MD Simulation Analysis: PFA

Pretty Fast Analysis (PFA) is a software suite for analyzing large-scale molecular dynamics (MD) simulation trajectory data on massively parallel supercomputers, GPU-based clusters, and traditional GPU-accelerated desktops.  PFA reads either CHARMM or AMBER style topology/trajectory files as input, and its analysis routines can scale up to thousands of compute cores or hundreds of GPU nodes with either parallel or UNIX file I/O.  Additionally, PFA has dynamic memory management, and each code execution can perform a variety of different structural, energetic, and file manipulation operations on a single MD trajectory at once.  The code itself has been written in a combination of Fortan90 and C, and its GPU kernels are written with NVidia's CUDA API to achieve maximum GPU performance.  To date, PFA has been tested and optimized for several TeraGrid resources including both Kraken and Ranger supercomputers, Lincoln and Longhorn GPU clusters, as well as numerous small cluster and desktop environments. PFA is produced by research staff at the Temple University Institute for Computational Molecular Science ( It is available for download here on the File Archive page.

Computational Cosmology: GADGET

GADGET is a freely available code for cosmological N-body/SPH simulations on massively parallel computers with distributed memory.

GADGET represents fluids by means of smoothed particle hydrodynamics (SPH). The code can be used for studies of isolated systems, or for simulations that include the cosmological expansion of space, both with or without periodic boundary conditions. In all these types of simulations, GADGET follows the evolution of a self-gravitating collisionless N-body system, and allows gas dynamics to be optionally included. Both the force computation and the time stepping of GADGET are fully adaptive, with a dynamic range which is, in principle, unlimited.

GADGET can therefore be used to address a wide array of astrophysically interesting problems, ranging from colliding and merging galaxies, to the formation of large-scale structure in the Universe. With the inclusion of additional physical processes such as radiative cooling and heating, GADGET can also be used to study the dynamics of the gaseous intergalactic medium, or to address star formation and its regulation by feedback processes.

Computational Biology: MrBayes

MrBayes is a program that is used to infer phylogeny through Bayesian inference.  The application, developed by John Huelsenbeck, Bret Larget, Paul van der Mark, Fredrik Ronquist, and Donald Simon, uses the Markov chain Monte Carlo (MCMC) technique to approximate the posterior probabilities of trees.  MrBayes is able to provide evolutionary models that can be used to analyze nucleotide, amino acid, restriction site, and morphological data.  Additional information about the application, as well as source code, can be found at the following URL:

Ocean Circulation: POP

POP is an ocean circulation model derived from earlier models of Bryan, Cox, Semtner and Chervin, in which depth is used as the vertical coordinate. The model solves the three-dimensional primitive equations for fluid motions on the sphere under hydrostatic and Boussinesq approximations. Spatial derivatives are computed using finite-difference discretizations which are formulated to handle any generalized orthogonal grid on a sphere, including dipole and tripole grids which shift the North Pole singularity into land masses to avoid time step constraints due to grid convergence. Time integration evolves the ocean model and can predict the evolution of properties of the oceans such as sea-surface height variability. POP is freely available to the community (under a copyright agreement); you can download the latest version from these pages.