md-simulations

There are 0 repository under md-simulations topic.

• markovmodel / pyemma_tutorials

  How to analyze molecular dynamics data with PyEMMA

  tutorialpyemmamd-simulationsanalysismolecular-dynamicskineticsmarkov-model
  Language:Jupyter Notebook 70

• MolSSI / covid

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

  covid-19covid19-datasars-cov-2molecular-dynamicsmolecular-dynamics-simulationmd-simulations
  Language:HTML 27

• seekrcentral / seekr2

  Simulation-Enabled Estimation of Kinetic Rates - Version 2

  condamd-simulationsnamd2openmmseekr2-openmm-plugin
  Language:Python 26

• bio-phys / PyDHAMed

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

  md-simulationssciencepythonfree-energyfree-energieskineticskinetic-modelingmolecular-dynamics
  Language:Jupyter Notebook 19

• 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.

  free-energy-calculationsinteractivemd-simulationspymol-pluginpythonpython3restraintssystem-generationtopology-building
  Language:Python 17
• addNewResidue.py

  kimjc95 / addNewResidue.py

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

  gromacsmolecular-dynamicsmolecular-dynamics-simulationcharmmcharmm-guiamberacpypesimulationmolecular-simulationmd-simulations
  Language:Python 8

• 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.

  md-simulationsproteinprotein-analysispythonrdfrdfssimulationvan-hove
  Language:Python 6

• Hekstra-Lab / mdtools

  Tools for running MD simulations in OpenMM

  md-simulationsmolecular-dynamicsopenmm
  Language:Python 6

• bakhshiali / Nano-Simulation

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

  lammpsmd-simulationsnanotechnologysimulation
  5

• bio-phys / kinetics-remd

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

  pythonsciencekineticsmd-simulationsremd-simulationskinetics-remdextracting-kinetics
  Language:Jupyter Notebook 5

• anyuzx / H5MD_Analysis

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

  molecular-dynamics-simulationlammpsmd-simulationsh5mdtrajectory-analysis
  Language:Cython 3

• gnikit / md-sim

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

  molecular-dynamicscoarse-grained-molecular-dynamicsfluid-simulationfluidmd-simulations
  Language:C++ 2

• 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.

  gromacsprotein-foldingprotein-dynamicsmd-simulationsmd-analysisstructure-based-model
  Language:Python 1

• 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

  amberambertoolscharmmenergy-calculationsgmx-mmgbsagmx-mmpbsagromacsmd-simulationsmmgbsammpbsanamd
  Language:Python 0

• Randika00 / Angular-Material-Main

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

  layoutcontainermd-simulationstypographyuicomponentspre-built-themes
  Language:TypeScript

• schlessinger-lab / LAT1-metainference

  Scirpts used for Metainference MD Simulations

  md-simulations
  Language:Python