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MD analysis
pyLFDA is a tool which allows analysis of pairwise lipid force distribution along with other functions such as curvature and diffusion.
Tools for analysis of Molecular Dynamics trajectories (based on the MDAnalysis and RDKit libraries)
a python package for the interfacial analysis of molecular simulations
A Python package for the analysis of molecular dynamics simulations.
Library of Python classes for parsing LAMMPS density profiles and data files, and specifically for post-processing of MD simulations of polymer brushes in equilibrium with solvent vapours.
Calculates the velocity autocorrelation function from a LAMMPS dump file
Calculates 3d structure factor and simulated x-ray diffraction pattern from molecular dynamics trajectories
Tools to calculate MSD on meshed surfaces from molecular dynamics
Files associated with Hall group publications
Post-Processing Polymer Molecular Dynamics Simulations
a Tcl code to calculate the 1D and 2D distributions of hydrogen bond density and strength
Python Implementation for Coulomb interactions
knnpe: A Python package implementing the k-nearest neighbor permutation entropy
python code to calculate inelastic-neutron-scattering dynamic structure factor, S(Q,w), from molecular dynamics trajectories using parallelism over Q-points.
Scripts for the analysis of interface-perpendicular diffusion in confined film or slit-pore geometries
Statistical inference of Generalized Langevin Equation using Expectation-Maximization algorithm
A python package for the extraction of memory kernels from time series
How to analyze molecular dynamics data with PyEMMA
Python 3 tool suite for the computation of position dependent memory kernels from time series.
Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.
Python script for calculating vibrational density of states (DOS) from LAMMPS dump file
Supporting material for the article
Tools and Tutorials of Molecular Simulations
MDAnalysis is a Python library to analyze molecular dynamics simulations.
Fortran and Python examples to accompany the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford University Press, 2017). Use the "Code" button, …
velocity.py reads in GROMACS trr trajectory (that inclides velocity information) and calculates center of mass translational velocity and angular velocity. It also computes translational and rotati…
The Active Matter Evaluation Package (AMEP) - a Python library for the analysis of particle-based and continuum simulation data of soft and active matter systems