md-simulations

There are 16 repositories under md-simulations topic.

  • markovmodel/pyemma_tutorials

    How to analyze molecular dynamics data with PyEMMA

    Language:Jupyter Notebook72910434

  • MolSSI/covid

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

    Language:HTML28102549

  • seekrcentral/seekr2

    Simulation-Enabled Estimation of Kinetic Rates - Version 2

    Language:Python275305

  • bio-phys/PyDHAMed

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

    Language:Jupyter Notebook194117

  • rinikerlab/restraintmaker

    Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation technique with coordinate-based particles). It can be used on a script layer or as an interactive plugin for PyMol. Features are different selection modes and Optimizers to distribute restraints.

    Language:Python17514
  • addNewResidue.py

    kimjc95/addNewResidue.py

    This code adds custom-made amino acids to the GROMACS forcefield directory.

    Language:Python8203

  • FZJ-JSC/speadi

    A Python package that aims to characterise the dynamics of local chemical environments from Molecular Dynamics trajectories of proteins and other biomolecules. Public mirror of https://gitlab.jsc.fz-juelich.de/slbio/speadi.

    Language:Python7401

  • Hekstra-Lab/mdtools

    Tools for running MD simulations in OpenMM

    Language:Python6222

  • bakhshiali/Nano-Simulation

    Molecular dynamics simulation of nano Structures, Materials and Properties using LAMMPS software.

    5101

  • bio-phys/kinetics-remd

    Extracting kinetics from replica exchange molecular dynamics and related methods that produce discontinuous trajectories.

    Language:Jupyter Notebook5314

  • anyuzx/H5MD_Analysis

    Analysis tool for H5MD file (HDF5 format for molecular dynamics simulation data)

    Language:Cython3000

  • gnikit/md-sim

    A mesh free molecular dynamics (MD) simulation for a fluid in an isothermal container

    Language:C++22180

  • c-sinner/sbm-tools

    sbm-tools is a simple python package for creating, modifying, and maintaining input files for native Structure-Based Model simulations to be used with the popular simulation software GROMACS.

    Language:Python1200

  • Randika00/Angular-Material-Main

    The simplest usage of the API, $theme: mat.define-theme() defines a theme with default values.

    Language:TypeScript0100

  • xBFreEnergy/xBFreE

    xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs

    Language:Python0201

  • schlessinger-lab/LAT1-metainference

    Scirpts used for Metainference MD Simulations

    Language:Python10