How to analyze molecular dynamics data with PyEMMA
-
Updated
May 29, 2019 - Jupyter Notebook
#
md-simulations
Here are 17 public repositories matching this topic...
MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store
-
Updated
Dec 16, 2023 - HTML
Simulation-Enabled Estimation of Kinetic Rates - Version 2
-
Updated
Oct 31, 2024 - Python
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
python science molecular-dynamics kinetics free-energy free-energies kinetic-modeling md-simulations
-
Updated
Mar 13, 2018 - Jupyter Notebook
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.
python interactive pymol-plugin python3 md-simulations free-energy-calculations restraints topology-building system-generation
-
Updated
Oct 27, 2022 - Python
This code adds custom-made amino acids to the GROMACS forcefield directory.
simulation molecular-dynamics molecular-simulation molecular-dynamics-simulation charmm gromacs amber md-simulations charmm-gui acpype
-
Updated
Aug 1, 2024 - Python
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.
-
Updated
Apr 25, 2024 - Python
Molecular dynamics simulation of nano Structures, Materials and Properties using LAMMPS software.
-
Updated
Feb 4, 2023
Tools for running MD simulations in OpenMM
-
Updated
Sep 12, 2023 - Python
Extracting kinetics from replica exchange molecular dynamics and related methods that produce discontinuous trajectories.
-
Updated
Jul 19, 2017 - Jupyter Notebook
Analysis tool for H5MD file (HDF5 format for molecular dynamics simulation data)
-
Updated
Jul 20, 2023 - Cython
A mesh free molecular dynamics (MD) simulation for a fluid in an isothermal container
-
Updated
May 31, 2020 - C++
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.
-
Updated
Mar 11, 2020 - Python
GRAVITy is an automated pipeline that streamlines molecular dynamics (MD) simulations. It allows users to simulate protein efficiently. It automates tasks like protein preparation, running simulations with GROMACS, and error handling, saving time and ensuring smooth execution.
bioinformatics simulation molecular-dynamics computational-biology bioinformatics-pipeline molecular-dynamics-simulation drug-discovery drug-repurposing md-simulations bioinformatics-tool
-
Updated
Dec 25, 2024 - Shell
xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs
charmm namd gromacs amber ambertools mmgbsa mmpbsa md-simulations energy-calculations gmx-mmpbsa gmx-mmgbsa
-
Updated
Nov 14, 2023 - Python
The simplest usage of the API, $theme: mat.define-theme() defines a theme with default values.
-
Updated
Aug 7, 2024 - TypeScript
Improve this page
Add a description, image, and links to the md-simulations topic page so that developers can more easily learn about it.
Add this topic to your repo
To associate your repository with the md-simulations topic, visit your repo's landing page and select "manage topics."