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make-graphitics

martini-polyelectrolytes

Generate Martini polyelectrolyte topology files for use with Gromacs

md6

C program for Molecular Dynamics. It implements the Verlet algorithm for only the positions. Periodic Boundary conditions.

md_ljp

An elementary MD simulation program written in python

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

meeko

Interfacing RDKit and AutoDock

mof_screen

High-throughput DFT of MOFs using ASE/VASP

molecular-dynamics

molecular-dynamics-simulation

Sample codes for my book on molecular dynamics simulation

moleculardynamicssimulation

Molecular dynamics simulation done as part of the course of Computational Physics at the master program of Applied Physics at TU Delft.

openff-forcefields

Force fields produced by the Open Force Field Initiative

optmaven_2.0

paratemp

A package for molecular dynamics analysis and parallel tempering in GROMACS

parmed

Parameter/topology editor and molecular simulator

pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

perses

REBFE _signle_dua topol _Experiments with expanded ensembles to explore chemical space

phaser

Phaser is a fun, free and fast 2D game framework for making HTML5 games for desktop and mobile web browsers, supporting Canvas and WebGL rendering.

programmingprojects

C++ Programming Tutorial in Chemistry

propnet

A knowledge graph for Materials Science.

protein_orientation

Protein orientation: Analysis of protein domain pitch

protocaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS

pylj

Teaching Utility for Classical Atomistic Simulation.

pytopol

A library for converting molecular topologies

qligfep

qmmm-workshop

Workshop teaching QMMM using Amber

raspa2

Classical molecular simulation code

restraintmaker

Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation technique with coordinate-based particles). It can be used on a script layer or as an interactive plugin for PyMol. Features are different selection modes and Optimizers to distribute restraints.

rip-md

sampl1

Repository for historical data from SAMPL1

simutil

Scripts and small programs to handle operations that support the treatment of data from the Molecular Dynamics (MD) software package DL_POLY (Classic).