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goodvibes

Calculate quasi-harmonic free energies from Gaussian output files with temperature and other corrections

grade

GRADE: A code to determine clathrate hydrate structures. GRADE analyzes atomic positions of water molecules to compute the number of 5(12), 6(2)5(12) and 6(4)5(12) cages and account for their three-dimensional structures. The output of GRADE can be used for visualization of clathrate hydrate evolution in trajectories using software such as VMD (Visual Molecular Dynamics). Four-body order parameter (F4) can also be calculated for trajectories.

graphtheroytrejctoryanalysis

gromacs

gromacs git repository

helmholtzmedia

Modelica library for the calculation of fluid properties from a Helmholtz energy equation of state (EoS).

htr

hts_workshop2019

Hands-on Introduction to Data Analysis for Genomics and Transcriptomics

indus

Implements the INDUS method for several probe volume geometries.

javascript-particle-system

2d JavaScript Particle System with gravity field simulation

lammps

Public development project of the LAMMPS MD software package

libgmxcpp

C++ toolkit for use in reading in and analyzing Gromacs files

ligpargen

A repository for tutorials and FAQ's about LigParGen

lumol

Universal extensible molecular simulation engine

matlab_real_space

Electronic structure code for molecules and clusters

mc-md-codes

Monte Carlo Simulation Code & Molecular Dynamics Code

mcmd

Monte Carlo and Molecular Dynamics Simulation Package

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

mdbenchmark

Quickly generate, start and analyze benchmarks for GROMACS and NAMD simulations.

mdms

MDMS: Molecular Dynamics Made Simple; Python program facilitating performing Molecular Dynamics simulations of proteins

mdsimulations

Simulation code

moleculardynamics

Simple Molecular Dynamics code for Discovery-Driven approach to real gas properties.

mpmc

A Monte Carlo molecular simulation software especially suited for polarizable models

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

openpathsampling

An open source Python framework for transition interface and path sampling calculations.

pdbe-molstar

Molstar PDBe implementation

pdbfixer

PDBFixer fixes problems in PDB files

phaseequilibriumwatericescan

Input files to reproduce the results of the paper: Phase equilibrium of water with hexagonal and cubic ice using the SCAN functional

plumed-nest

Draft nest

plumed.github.io

PLUMED website

plumed2

Development version of plumed 2