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

Monte Carlo and Molecular Dynamics Simulation Package

UF3: a python library for generating ultra-fast interatomic potentials

A hierarchical, component based molecule builder

Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure

HMM implementation featuring Deal.II (FE) and LAMMPS (MD)

AdaptivePELE is a Python package aimed at enhancing the sampling of molecular simulations

Contact map analysis for biomolecules; based on MDTraj

The repository pymolschortucts contains the a collection of shortcuts that are loaded on startup of PyMOL. These shortcuts enable websearches from within PyMOL as well as many other convienent functions that make work in PyMOL more productive..

Protein Secondary Structure predictor using Convolutional Neural Networks

Weighted Ensemble simulation framework in Python

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

A script to build reference datasets for training neural network potentials from given LAMMPS trajectories.

Debug Python code within a Docker container remotely from your terminal using pudb

Just another tool to download specify Symbol (.pdb) files

A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.

Converts between Windows PDB and Portable PDB formats.

Experiments with expanded ensembles to explore chemical space

NoPdb: Non-interactive Python Debugger

A library to open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files in Rust.

Modeling molecular ensembles with scalable data structures and parallel computing

Benchmarking common tasks on proteins in various languages and packages

NequIP is a code for building E(3)-equivariant interatomic potentials

TeamCity Symbol Server plugin

The source of the votca-csg and xtp packages

MOLeculAR structure annoTator

Utility to resolve SQL Server callstacks to their correct symbolic form using just PDBs and without a dump file

quantum-dynamics-hub.github.io/libra/index.html

Python interface of cpptraj

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

PDB parser in Haskell

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

Tinker9: Next Generation of Tinker with GPU Support

Fetch PDB symbols directly from Microsoft's symbol servers

In silico chemical library engine for high-accuracy chemical property prediction

A package for atom-typing as well as applying and disseminating forcefields

Remotely and collaboratively debug your Python application via an IRC channel.

High-performance operations for neural network potentials

How to analyze molecular dynamics data with PyEMMA

Pytorch differentiable molecular dynamics

Protein structure comparison tools such as SSAP and SNAP

Quantum mechanic mass spectrometry calculation program

Protein cavity identification and automatic subpocket decomposition

Packmol - Initial configurations for molecular dynamics simulations

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

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

RosettaDesign using PyRosetta

A Python library and command line interface for automated free energy calculations

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

Physical validation of molecular simulations

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.

Molecular dynamics simulation software

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

Single Page Web Application for displaying and studying molecular models

Tinker: Software Tools for Molecular Design

Tool to build force field input files for molecular simulation.

Teaching Utility for Classical Atomistic Simulation.

SchNetPack - Deep Neural Networks for Atomistic Systems

HOOMD-blue example scripts.

VSCode Extension for interactively visualising protein structure data in the editor

RXMD : Linear-Scaling Parallel Reactive Molecular Dynamics Simulation Engine