121 Open source projects that are alternatives of or similar to Mdtraj

Python interface of cpptraj

Development version of plumed 2

sGDML - Reference implementation of the Symmetric Gradient Domain Machine Learning model

Variational Autoencoder for Dimensionality Reduction of Time-Series

PDB parser in Haskell

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

Quickly generate, start and analyze benchmarks for molecular dynamics simulations.

Notebook-integrated tools for molecular simulation and visualization

Tinker9: Next Generation of Tinker with GPU Support

Powerful, efficient particle trajectory analysis in scientific Python.

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GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools (v4.6.x, v5.x, 2016.x, 2018.x, 2019.x, all with the same Python code) into python scripts.

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[email protected] COVID-19 efforts

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😎 A curated list of awesome Molecular Dynamics libraries, tools and software.

How to analyze molecular dynamics data with PyEMMA

a python package for the interfacial analysis of molecular simulations

Pytorch differentiable molecular dynamics

Qball (also known as [email protected]) is a first-principles molecular dynamics code that is used to compute the electronic structure of atoms, molecules, solids, and liquids within the Density Functional Theory (DFT) formalism. It is a fork of the Qbox code by Francois Gygi.

Protein structure comparison tools such as SSAP and SNAP

A CUDA project for Molecular Dynamics, Brownian Dynamics, Hydrodynamics... intended to simulate a very generic system constructing a simulation with modules.

Quantum mechanic mass spectrometry calculation program

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

Protein cavity identification and automatic subpocket decomposition

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

Packmol - Initial configurations for molecular dynamics simulations

Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format

Enables computations over a set of particles in N-dimensional space

Pdb and Vim integration

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

Tool for PDB generation from IDA Pro database

RosettaDesign using PyRosetta

A cheatsheet for the Python Debugger (pdb)

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Full-screen console debugger for Python

MDToolbox.jl: A Julia package for molecular dynamics trajectories analysis and modeling of biomolecules

A parser for Microsoft PDB (Program Database) debugging information

Physical validation of molecular simulations

pdb + Rich library

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.

Some useful Tips and Tricks to speed up the data analysis process in Python.

Molecular dynamics simulation software

gevent tools

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

A simple tutorial about effectively using pdb

Single Page Web Application for displaying and studying molecular models

ReClassEx

Tinker: Software Tools for Molecular Design

Tool to build force field input files for molecular simulation.

SchNetPack - Deep Neural Networks for Atomistic Systems

HOOMD-blue example scripts.

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RXMD : Linear-Scaling Parallel Reactive Molecular Dynamics Simulation Engine

Application to assign secondary structure to proteins

Syntax highlighting for computational biology