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    38 repositories

    • mftoid-rev-residues

      Public
      Pfaendtner + Ferguson research team collaboration building library of residues based on the Weiser+Santiso revised MFTOID force field
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • cgen2gmx

      Public
      command line for organizing force field parameters for MD simulations (GROMACS)
      Python
      •
      MIT License
      •1•0•0•0•Updated Sep 3, 2024Sep 3, 2024

    • plumed2

      Public
      Development version of plumed 2
      C++
      •
      GNU Lesser General Public License v3.0
      •289•0•0•0•Updated Sep 21, 2022Sep 21, 2022

    • Nance_Enzyme_Encap_MD

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Aug 24, 2022Aug 24, 2022

    • dcmlp

      Public
      repo of data conversion for training machine learning potentials. this tool will work for all data and I'm gonna rule the world
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 9, 2022Jul 9, 2022

    • PRGNESTS

      Public
      Home for our PLUMED-NEST repos: https://www.plumed-nest.org/
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 3, 2022Jun 3, 2022

    • ek-conformation-project

      Public
      python analysis scripts for EK/G conformation project
      Jupyter Notebook
      •0•0•0•0•Updated May 2, 2022May 2, 2022

    • Coco_Code

      Public
      Coco's codes collection from PRGs
      Jupyter Notebook
      •0•0•0•0•Updated Apr 30, 2022Apr 30, 2022

    • peptoid-ffgen

      Public
      Generates MFTOID parameters for peptoids from a DFT scan
      Python
      •
      MIT License
      •2•0•0•0•Updated Feb 25, 2022Feb 25, 2022

    • transition-sampling

      Public
      Python
      •
      MIT License
      •0•2•3•1•Updated Jan 7, 2022Jan 7, 2022

    • Electrolyte-at-interface

      Public
      This repository hosts the input files for the electrolyte/electrode interface paper
      MIT License
      •0•0•0•0•Updated Sep 12, 2021Sep 12, 2021

    • Cat_NPs_HIP_project

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 31, 2021Aug 31, 2021

    • gcp-gromacs

      Public
      Scripts for setting up a high-throughput gromacs compute engine on Google Cloud Platform
      HCL
      •
      MIT License
      •0•0•0•0•Updated Aug 17, 2021Aug 17, 2021

    • BETO_NLP

      Public
      Repo for working on the NLP project and will try to keep it neat.
      Python
      •
      MIT License
      •2•3•2•0•Updated Mar 29, 2021Mar 29, 2021

    • pbut_tica-msm

      Public
      tICA used to build MSMs for the study of protein bound uremic toxins
      Roff
      •0•3•0•0•Updated Mar 17, 2021Mar 17, 2021

    • Python

      Public
      Tools and tutorials for python
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Jan 6, 2021Jan 6, 2021

    • aimless_shooting

      Public
      Python
      •
      MIT License
      •0•1•1•0•Updated Nov 2, 2020Nov 2, 2020

    • UWPRG.github.io

      Public
      Group website for PRG -
      HTML
      •
      MIT License
      •0•0•4•0•Updated Sep 16, 2020Sep 16, 2020

    • pbut_analysis

      Public
      Analysis scripts for MD simulations of protein bound uremic toxins
      Roff
      •0•0•0•0•Updated Aug 10, 2020Aug 10, 2020

    • UW-Molecular-Data-Mining

      Public
      Repository for chemical data extraction from literature corpora
      HTML
      •
      MIT License
      •8•4•0•0•Updated Jul 29, 2020Jul 29, 2020

    • GROMACS

      Public
      Tools, tutorials, and wiki for GROMACS
      Python
      •
      MIT License
      •9•18•0•1•Updated Jul 21, 2020Jul 21, 2020

    • Paper_bot

      Public
      A powerful AI that bugging people of our achievement in science
      Jupyter Notebook
      •0•0•0•0•Updated Jul 17, 2020Jul 17, 2020

    • Gaussian

      Public
      Tools, tutorials, and wiki for Gaussian
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 8, 2020Jul 8, 2020

    • MOLSIM-2020

      Public
      Repository for students enrolled in Molsim Winter 2020
      Jupyter Notebook
      •
      MIT License
      •7•0•0•0•Updated Mar 22, 2020Mar 22, 2020

    • Neural-Network-Potentials

      Public
      MIT License
      •0•0•0•0•Updated Jan 31, 2020Jan 31, 2020

    • MOLSIM

      Public
      Repository for the group class on Molecular Simulation
      Jupyter Notebook
      •1•2•0•0•Updated Mar 25, 2019Mar 25, 2019

    • cookiecutter-molecular-dynamics

      Public
      cookiecutter template for molecular dynamics projects with GROMACS and Plumed
      Python
      •1•2•0•0•Updated Nov 13, 2018Nov 13, 2018

    • Plumed

      Public
      Scripts, tools for using PLUMED for enhanced sampling techniques in molecular simulation
      1•4•0•0•Updated Sep 10, 2018Sep 10, 2018

    • tutorials

      Public
      Tutorials and associated scripts from the Pfaendtner group
      MIT License
      •0•0•2•0•Updated Aug 16, 2018Aug 16, 2018

    • CP2K

      Public
      1•1•0•0•Updated Jun 13, 2018Jun 13, 2018