Software
SolvMol
This is a serial code written in fortran90 by Dmitry Matyushov and David LeBard that performs calculations of the free energy of polar solvation. The algorithm defines a molecule in terms of atomic coordinates or atomic groups and a set of partial charges, and the solvent in terms of a solvent response function built upon longitudinal and transverse dipolar polarization structure factors.
Pretty Fast Analysis
Pretty Fast Analysis (PFA) is an ‘embarrassingly parallel’ software suite written by David LeBard in fortran90/C/MPI with Nvidia 's CUDA API and the openCL framework for access to GPU threads. This software analyzes energetic and structural data from large-scale molecular dynamics trajectories. The code has been tested on small CPU/GPU clusters (< 50 CPUs/GPUs), medium sized CPU/GPU clusters (< 4000 CPU, < 200 GPU), and large supercomputing environments (60,000+ cores), and results appear encouraging on every level.
HOOMD-Blue
Highly Optimized Object Oriented Molecular Dynamics (HOOMD) Blue version is a general molecular dynamics code first written in C++ by Joshua Anderson at Ames Laboratory for Nvidia GPU's, now at the University of Michigan. From version 0.8.2 on, HOOMD-Blue contains several potentials for both the CPU and GPU written by David LeBard and colleagues including angle bending, harmonic torsions, harmonic improper torsions, coarse grain angle potentials with angle corrections, and several optimizations for force-field exclusion mappings.