...
RStudio
RStudio is a free and open source integrated development environment(IDE) for R.
Gromacs
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
Desmond
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems.
PetSc
PetSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for parallelism. Note, another useful link to visit. PetSc has a complex build environment that allows one to include various applications. We encourage interested users to build the suite of interest in their home directory. Installation instructions for a particular set of applications can be found here
...