LAMMPS

LAMMPS is a molecular dynamics (MD) code used to simulate the properties of fluids, solids, and molecules.

I contributed to LAMMPS KOKKOS package, which enables certain LAMMPS kernels (pair and fix styles, neighbor list building, inter-processor communication) to run efficiently on accelerator hardware, including GPUs and many-core chips (via OpenMP or pthreads).

Source: git webpage

VOTCA

VOTCA is a versatile object oriented toolkit for coarse-graining applications which focuses on the analysis of molecular dynamics data, the development of the systematic coarse-graining techniques as well as methods used for simulating microscopic charge transport in disordered semiconductors. Its C++ core is interfaced to bash and perl flow-control scripts.

I am a contributor to the VOTCA project. My main contribution, so far, to the project is the implementation of relative entropy-based coarse-graining technique [J. Chem. Phys., 134, 094112, 2011]. In article J. Chem. Phys., 137, 214707, 2012 [pdf], coarse-grained potentials for water confined inside a graphene nano-channel are systematically optimized by relative entropy minimization using VOTCA.

Source: googlecode webpage

Local Pressure from GROMACS

Source: github

My GitHub

My Ohloh Profile

Ohloh profile for sikandar y. mashayak

Helpful Coding References