85 Open source projects that are alternatives of or similar to pytraj

Tensorflow + Molecules = TensorMol

The ESPResSo package

Packmol - Initial configurations for molecular dynamics simulations

Tool to build force field input files for molecular simulation.

Collective variables module for molecular simulation and analysis programs

Contact map analysis for biomolecules; based on MDTraj

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

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

🏗 Statistical models for biomolecular dynamics 🏗

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

Formed trajectories of sets of points.Experimented on finding similarities between trajectories based on DTW (Dynamic Time Warping) and LCSS (Longest Common SubSequence) algorithms.Modeled trajectories as strings based on a Grid representation.Benchmarked KNN, Random Forest, Logistic Regression classification algorithms to classify efficiently t…

the simple alchemistry library

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

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

Teaching Utility for Classical Atomistic Simulation.

The chemistry library you were waiting for

Quantum mechanic mass spectrometry calculation program

Molecular dynamics and Monte Carlo soft matter simulation on GPUs.

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

Universal extensible molecular simulation engine

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

End-To-End Molecular Dynamics (MD) Engine using PyTorch

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

LOOS: a lightweight object-oriented structure analysis library

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

Molecular dynamics simulation software

Monte Carlo and Molecular Dynamics Simulation Package

A hierarchical, component based molecule builder

Python package designed for collecting and processing trajectory data.

The source of the votca-csg and xtp packages

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

High-performance operations for neural network potentials

Folding@home GPU benchmark

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

🚂 Python API for Emma's Markov Model Algorithms 🚂

Pytorch differentiable molecular dynamics

Development version of plumed 2

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

Variational Autoencoder for Dimensionality Reduction of Time-Series

Python tools for spatial trajectory and time-series data analysis

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

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

Notebook-integrated tools for molecular simulation and visualization

Modeling molecular ensembles with scalable data structures and parallel computing

Powerful, efficient particle trajectory analysis in scientific Python.

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

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.

Weighted Ensemble simulation framework in Python

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

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

Molecular simulation in Julia

天池DCIC2020船只轨迹数据挖掘比赛算法阶段Rank 3解决方案：

[email protected] COVID-19 efforts

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

Physical validation of molecular simulations

Tinker9: Next Generation of Tinker with GPU Support

Experiments with expanded ensembles to explore chemical space

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

GREIN : GEO RNA-seq Experiments Interactive Navigator

MDAnalysis tool to calculate membrane curvature.