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36 search results found

pyiron - an integrated development environment (IDE) for computational materials science.

Variational Autoencoder for Dimensionality Reduction of Time-Series

Python interface of cpptraj

Drug Computing ⭐ 131

Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.

Molecular Design Toolkit ⭐ 131

Notebook-integrated tools for molecular simulation and visualization

Molecular Dynamics Simulation ⭐ 122

Sample codes for my book on molecular dynamics simulation

Quantum Mechanics ⭐ 56

A collection of interactive notebooks to explain concepts of quantum mechanics and related topics

Litmatter ⭐ 55

Rapid experimentation and scaling of deep learning models on molecular and crystal graphs.

Unsupervised learning of atomic scale dynamics from molecular dynamics.

N-Dimensional MD engine with symmetry group constraints

Structural Bioinformatics ⭐ 34

This repository includes the slides and the practicals for the course of Structural Bioinformatics of the MBB/QB degrees at the University of Milano, originally inspired by https://github.com/pb3lab/ibm3202

Lstm Predict Md ⭐ 30

Learning Molecular Dynamics with Simple Language Model built upon Long Short-Term Memory Neural Network

Pyemma_tutorials ⭐ 29

How to analyze molecular dynamics data with PyEMMA

Hoomd Examples ⭐ 28

HOOMD-blue example scripts.

IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook

Analyse Nucleic Acids Structure and Simulations with baRNAba

Ambertools Openmm Md ⭐ 24

Open Source, Mostly just clicking mouse to finish a simulation with Ambertools and OpenMM. It was designed to use locally but another notebook to finish the simulaiton on Colab was attached as well.

Mdnotebooks ⭐ 22

Jupyter Notebooks for Molecular Dynamics

Coarse Graining Auto Encoders ⭐ 21

Pydhamed ⭐ 17

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations

Peggenerator ⭐ 17

Generate PEG topology for GROMACS and LAMMPS

Teaching Utility for Classical Atomistic Simulation.

Openmm Tutorials ⭐ 15

Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM

Moleculardynamics ⭐ 14

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

Namd Fep ⭐ 14

Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is probably one of the fastest FEP simulation with FREE GPU hardwares that the genearl public could have access to

Freud Examples ⭐ 13

Examples for the freud library.

Newma Md ⭐ 11

Conformational exploration SARS-CoV-2 (coronavirus responsible for COVID-19)

Pydiffusion ⭐ 10

Analyse Rotational Diffusion Tensor from MD Simulations

Mosdef Workflows ⭐ 9

Sample molecular simulation workflows using a MoSDeF and community tools

How To Lammps ⭐ 9

How-to perform LAMMPS simulations

Gromacs On Colab ⭐ 8

Google Colab notebooks for running molecular dynamics simulations with GROMACS

Optimus_bind_sample ⭐ 7

Designed to optimize the time/accuracy trade-off in predicting the effects of mutations on protein-protein binding

Accelerated Weighted Ensemble (AWE) provides a Python library for adaptive sampling of molecular dynamics.

Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics.

Old Lammps Inputs ⭐ 7

LAMMPS tutorials for both beginners and advanced users

In silico platform to analize MD trajectories using metrics, clustering and machine&deep learning techniques

Este repositorio debe ser el punto de partida y encuentro para cualquier investigador o estudiante que quiera comenzar a trabajar con/en la UIBCDF. Si has caído aquí por otro motivo y este material te es útil, eres más que bienvenido a usarlo e interaccionar con nosotros.

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