M

molecular dynamics

The GROMACS molecular simulation toolkit.

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.

Analyse molecular dynamics simulations of interfacial and confined systems.

A python tool box for GPUMD simulations

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.

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

Dynamical structure factors and correlation functions from molecular dynamics trajectories

An unsupervised learning program for analyzing molecular dynamics data

High-order force constants for the masses

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

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

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