74 Open source projects that are alternatives of or similar to Pnerf

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

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

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

Pytorch differentiable molecular dynamics

Molecular dynamics and Monte Carlo soft matter simulation on GPUs.

Experiments with expanded ensembles to explore chemical space

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.

The chemistry library you were waiting for

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

High-performance operations for neural network potentials

Universal extensible molecular simulation engine

Tinker9: Next Generation of Tinker with GPU Support

Packmol - Initial configurations for molecular dynamics simulations

HOOMD-blue example scripts.

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

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

Tool to build force field input files for molecular simulation.

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

Tensorflow + Molecules = TensorMol

Teaching Utility for Classical Atomistic Simulation.

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

How to analyze molecular dynamics data with PyEMMA

The ESPResSo package

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

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

Powerful, efficient particle trajectory analysis in scientific Python.

Python interface of cpptraj

Contact map analysis for biomolecules; based on MDTraj

SchNetPack - Deep Neural Networks for Atomistic Systems

Quantum mechanic mass spectrometry calculation program

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

Modeling molecular ensembles with scalable data structures and parallel computing

OpenMM is a toolkit for molecular simulation using high performance GPU code.

Weighted Ensemble simulation framework in Python

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

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

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

Molecular dynamics simulation software

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

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

A plugin that allows the use of Tensorflow in Hoomd-Blue for GPU-accelerated ML+MD

Folding@home GPU benchmark

The source of the votca-csg and xtp packages

🚂 Python API for Emma's Markov Model Algorithms 🚂

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

Development version of plumed 2

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

Variational Autoencoder for Dimensionality Reduction of Time-Series

A curated list of Python packages related to chemistry

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

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

Notebook-integrated tools for molecular simulation and visualization

Tinker: Software Tools for Molecular Design

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

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

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

An open library for the analysis of molecular dynamics trajectories

RXMD : Linear-Scaling Parallel Reactive Molecular Dynamics Simulation Engine

A hierarchical, component based molecule builder