markovmodel/pyemma_tutorials

How to analyze molecular dynamics data with PyEMMA

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bio-phys/nix-lir-binding-to-wipi2d

Language: Jupyter Notebook - Size: 90.8 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

hopanoid/Enzyme-Reaction-Dynamics-Tutorial

A QM-MM Tutorial of Enzyme Reaction Dynamics

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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: Python - Size: 1.02 MB - Last synced at: 19 days ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 1

Randika00/Angular-Material-Main

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

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seekrcentral/seekr2

Simulation-Enabled Estimation of Kinetic Rates - Version 2

Language: Python - Size: 28.4 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 27 - Forks: 6

kimjc95/addNewResidue.py

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

Language: Python - Size: 2.79 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 8 - Forks: 2

MolSSI/covid

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

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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: Python - Size: 32.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

Hekstra-Lab/mdtools

Tools for running MD simulations in OpenMM

Language: Python - Size: 253 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 3

gnikit/md-sim

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

Language: C++ - Size: 62.4 MB - Last synced at: about 1 month ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 0

bio-phys/PyDHAMed

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

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schlessinger-lab/LAT1-metainference

Scirpts used for Metainference MD Simulations

Language: Python - Size: 679 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

bakhshiali/Nano-Simulation

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

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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: Python - Size: 34 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 3

bio-phys/kinetics-remd

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

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anyuzx/H5MD_Analysis

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

Language: Cython - Size: 702 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0

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: Python - Size: 685 KB - Last synced at: 4 months ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0