jlefman

jlefman's Stars

• zarr-developers/zarr-specs

  Zarr core protocol for storage and retrieval of N-dimensional typed arrays

  8728

• nwchemgit/nwchem

  NWChem: Open Source High-Performance Computational Chemistry

  Language:Fortran499161

• mdtraj/mdtraj

  An open library for the analysis of molecular dynamics trajectories

  Language:Python586279

• deepmodeling/deepmd-kit

  A deep learning package for many-body potential energy representation and molecular dynamics

  Language:C++1.5k504

• khavernathy/mcmd

  Monte Carlo and Molecular Dynamics Simulation Package

  Language:C++8318

• choderalab/openmmtools

  A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

  Language:Python24777

• choderalab/yank

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

  Language:Python17870

• openforcefield/openff-toolkit

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

  Language:Python31190

• Colvars/colvars

  Collective variables library for molecular simulation and analysis programs

  Language:C++20559

• atomistic-machine-learning/schnetpack

  SchNetPack - Deep Neural Networks for Atomistic Systems

  Language:Python773214

• jparkhill/TensorMol

  Tensorflow + Molecules = TensorMol

  Language:Python27175

• openmm/openmm

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

  Language:C++1.5k519

• plumed/plumed2

  Development version of plumed 2

  Language:C++357283

• gromacs/gromacs

  Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.

  Language:C++697326

• glotzerlab/hoomd-blue

  Molecular dynamics and Monte Carlo soft matter simulation on GPUs.

  Language:C++334130

• QEF/q-e

  Mirror of the Quantum ESPRESSO repository. Please do not post Issues or pull requests here. Use gitlab.com/QEF/q-e instead.

  Language:Fortran563280

• lammps/lammps

  Public development project of the LAMMPS MD software package

  Language:C++2.2k1.7k

• tbepler/topaz

  Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.

  Language:Jupyter Notebook17063

• 3dem/relion

  Image-processing software for cryo-electron microscopy

  Language:C++445200