M

molecular dynamics

The GROMACS molecular simulation toolkit.

A python tool box for GPUMD simulations

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

Dynamical structure factors and correlation functions from molecular dynamics trajectories

The project provides Python tool-chain and shell scripts for molecular simulation workflows: preparation, running and analysing molecular dynamics (MD) simulations of bio- and organic soft condensed matter.

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

Sea Urchin is an algorithm that combines dimensionality reduction (UMAP), unsupervised hierarchical clustering (HDBSCAN) and structural alignment (FASTOVERLAP) to quantitatively characterize prevalent coordination environments of chemical species within MD data.

High-order force constants for the masses

An unsupervised learning program for analyzing molecular dynamics data

mdinterface: A Python package to build interface systems for Molecular Dynamics simulations

Implementation of a Langevin bath and DPD solvent, analysis of its properties and comparison of the results obtained using these two models. Based on a Molecular Dynamics code previously developed, modified to get a Langevin Dynamics (LD) code and then, a Dissipative Particle Dynamics (DPD) code for a simple fluid.

Simple Van der Waals gas simulation program written in Fortran. Includes a serial code version and a version parallelized using OpenMPI.

A computational physics coursework repository of:

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

Implement molecular dynamics to investigate the formation of Lennard-Jones clusters.

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.

Computational exercise for the Polymer Theory course @ University of Vienna

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*

Webpage of workshop http://baltichpc.gitlab.io/