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73 search results found

Mdanalysis ⭐ 1,154

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Cuda Programming ⭐ 955

Sample codes for my CUDA programming book

Graphics Processing Units Molecular Dynamics

Examples ⭐ 265

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, or follow the "Releases" link below.

Python implementation of the multistate Bennett acceptance ratio (MBAR)

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

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 dynamics simulation software

Molecular Dynamics Simulation ⭐ 122

Sample codes for my book on molecular dynamics simulation

Nbodysimulator.jl ⭐ 122

A differentiable simulator for scientific machine learning (SciML) with N-body problems, including astrophysical and molecular dynamics

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

RadonPy is a Python library to automate physical property calculations for polymer informatics.

Celllistmap.jl ⭐ 76

Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbor lists, etc.

Monte Carlo and Molecular Dynamics Simulation Package

Lammpstutorials.github.io ⭐ 65

LAMMPS tutorials for both beginners and advanced users

Solarsystem ⭐ 49

A solar system simulator with Verlet, using OpenGL for displaying.

Ensembler ⭐ 44

Automated omics-scale protein modeling and simulation setup.

PyRod - Tracing water molecules in molecular dynamics simulations

MiniMD Molecular Dynamics Mini-App

Seams Core ⭐ 29

The d-SEAMS C++ core engine

Mdsynthesis ⭐ 29

a logistics and persistence engine for the analysis of molecular dynamics trajectories

Membrane Curvature ⭐ 26

MDAnalysis tool to calculate membrane curvature.

MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store

Corrections ⭐ 23

Corrections to the text of the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford University Press, 2017)

Visualdynamics ⭐ 23

Web Platform made with Python and NextJS for automating GROMACS simulations

Autoforce ⭐ 23

Sparse Gaussian Process Potentials

Propkatraj ⭐ 23

pKa estimates for proteins using an ensemble approach

Real time molecular dynamics in the browser using LAMMPS

Ls1 Mardyn ⭐ 22

ls1-MarDyn is a massively parallel Molecular Dynamics (MD) code for large systems. Its main target is the simulation of thermodynamics and nanofluidics. ls1-MarDyn is designed with a focus on performance and easy extensibility.

Ligpargen ⭐ 22

Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.

Polymer Molecular Dynamics ⭐ 21

Perform high-throughput polymer molecular dynamics simulations with ease

⚡ general purpose coarse-grained molecular dynamics simulation package

Protocaller ⭐ 18

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

Rmd_digging ⭐ 18

RMD_digging is aimed to provide pre-processing and post-processing tools for the reactive molecular dynamics (ReaxFF) simulations based on MATLAB language, including formatting the reactive force field parameters, statistic anasysis of structures, trajectories and mechanisms and output of the visualization files.

A codebase for classical molecular dynamics (MD) simulation setup and results analysis.

Do_x3dna ⭐ 17

To analyze fluctuations in DNA or RNA structures in molecular dynamics trajectories.

CHAP is a tool for the functional annotation of ion channel structures:

Adaptivemd ⭐ 16

A python framework to run adaptive Markov state model (MSM) simulation on HPC resources

Eventmoleculardynamics ⭐ 15

A program implementing event driven molecular dynamics for hard smooth spheres, using OpenGL for displaying

Python bindings for TNG file format

Command line interface for MDAnalysis

Waternetworkanalysis ⭐ 13

Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis

Complexmixtures.jl ⭐ 12

Package to perform minimum-distance distribution analyses of complex solute-solvent interactions

Molecular Simulation ⭐ 12

分子シミュレーションの理論や関連するトピックをまとめたノート

Sarkas Python MD suite for Dense Plasmas Physics

Molsysmt ⭐ 11

Open source library to work with molecular systems

SAPT energy calculator built using MDAnalysis and Psi4

Tools to calculate descriptors from molecular dynamics and it's application to predict drug resistance.

Mode Task ⭐ 10

PCA and normal mode analysis of proteins

Celllists.jl ⭐ 10

Julia language implementation of the Cell Lists algorithm to solve the fixed-radius near neighbors problem including serial and multithreaded algorithms.

Automated generation of LAMMPS data and input files for polymer neural network molecular dynamics simulations

💻 Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters.

An open-source tool for building initial structures for bio-membranes and drug-delivery systems.

Scripts to prepare and analyze molecular dynamics simulations

Open Source, Prepare a molecular dynamic simulation from scratch without installing local VMD, use LigParGen for topology, it is one of the most reliable MD for a general solution protein-ligand simulation.

Stochastic ⭐ 8

Pychastic is a stochastic differential equations integrator written entirely in python.

mirrored from https://gitlab.com/ccp5/dl-poly/

Neuro Visor ⭐ 8

A research tool based in virtual reality. Produced by the Center for Computational Mathematics and Modeling at Temple University

Transport_tools ⭐ 7

a library for massive analyses of internal voids in biomolecules and ligand transport through them

This repository contains the code for simulating the growth of a Biofilm after attachment using Molecular dynamics simulation methods. The project was build as part of the iGEM 2020 Contest. The BiofilmSimulation software can be installed as A python package, documented under https://pypi.org/project/BiofilmSimulation.

Old Lammps Inputs ⭐ 7

LAMMPS tutorials for both beginners and advanced users

Gromacstutorials.github.io ⭐ 7

Repository of the gromacstutorials webpage

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

Proton exchange in solvent molecules using openMM

asyncmd is a library to write concurrent code for setup, run and analysis of molecular dynamics simulations using pythons async/await synthax.

Program that implements assembling and disassembling of microtubules

Python interface for Enhanced Monte Carlo (EMC)

Python tool to submit several PBS jobs on the HPC

Rotamerconvolvemd ⭐ 6

Analysis of molecular dynamics trajectories or conformational ensembles in terms of spin-label distances as probed in double electron-electron resonance (DEER) experiments.

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.

Projectraccoon ⭐ 5

Automated construction of atomistic and coarse-grained models in the PDB format for polymer peptide conjugates.

Molecular_dynamics ⭐ 5

A 3D interactive program for molecular dynamics

1-73 of 73 search results

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