M

molecular dynamics

The GROMACS molecular simulation toolkit.

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

A modification of GROMACS that implements the "chain coordinate", a reaction coordinate for pore formation in membranes and stalk formation between membranes

A computational physics coursework repository of:

Non-linear ODE solvers, Lattice Boltzmann Method (LBM), Direct Simulation Monte Carlo (DSMC), Molecular Dynamics (MD)

Manybody DPD (https://journals.aps.org/pre/pdf/10.1103/PhysRevE.68.066702) with two evaporation protocols. The code is accelerated if running on a Nvidia GPU.

SC-MD: A Shift/Collapse (SC) Hybrid MPI/OpenMP/GPU/MIC Molecular Dynamics Code for Many-Body Potentials

SC-MD is a fast and highly scalable molecular dynamics (MD) simulator specialized for many-body potential on large-scale computing platforms.

provide some trajecctory analysis code for gromacs-202*

High-performance Matrix calculation code for ECPM molecular dynamic simulation

Compute the pair correlation of a configuration of particles using OpenCL on a GPU.

COSIRMA (COmputer Simulator for IRradiation of MAterials)

Graphical User Interface for simulating ion irradiation of materials with molecular dynamics using PARCAS. The project is being developed at the University of Helsinki.

Tools for the analysis of Molecular Dynamics Simulations