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Jan 19, 2021 - Python
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molecular-dynamics-simulation
Here are 121 public repositories matching this topic...
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
python
science
molecular-dynamics
computational-chemistry
molecular-simulation
molecular-dynamics-simulation
trajectory-analysis
mdanalysis
Sample codes for my CUDA programming book
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Nov 28, 2020 - Cuda
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
python
molecular-dynamics
openmm
molecular-dynamics-simulation
drug-discovery
free-energy
free-energy-perturbation
alchemical-free-energy-calculations
mskcc
alchemical
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Nov 15, 2020 - Python
Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
python
monte-carlo
molecular-dynamics
solubility
molecular-dynamics-simulation
drug-discovery
docking
ligand-screening
teaching-materials
educational-software
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Mar 5, 2020 - HTML
Graphics Processing Units Molecular Dynamics
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Jan 18, 2021 - Cuda
A differentiable simulator for scientific machine learning (SciML) with N-body problems, including astrophysical and molecular dynamics
automatic-differentiation
molecular-dynamics
molecular-dynamics-simulation
geometric-algorithms
algorithmic-differentiation
differentiable-programming
symbolic-integration
scientific-machine-learning
sciml
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Dec 29, 2020 - Julia
Monte Carlo and Molecular Dynamics Simulation Package
crystal
chemistry
atomic
pdb
physics
monte-carlo
molecular-dynamics
molecular-simulation
molecular-dynamics-simulation
monte-carlo-simulation
crystal-structure
physics-simulation
molecules
monte-carlo-simulations
gas-model
gas-dynamics
xyz
periodicity
polarization
nvt
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Oct 10, 2020 - C++
A Python Library for Reading, Writing, and Converting Computational Chemistry File Formats
json-schema
molecular-dynamics
computational-biology
computational-chemistry
molecular-simulation
computational-physics
molecular-dynamics-simulation
file-converter
quantum-chemistry
file-conversion
quantum-chemistry-programs
data-parsing
molecular-mechanics
input-output
file-format-converter
file-formats
theoretical-chemistry
file-format-library
quantum-chemistry-packages
molecular-electronic-structure
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Oct 26, 2020 - Python
Automated omics-scale protein modeling and simulation setup.
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Dec 31, 2016 - Python
A solar system simulator with velocity Verlet, using OpenGL for displaying.
opengl
lightning
shaders
xml
physics
planet
molecular-dynamics
moon
computational-physics
molecular-dynamics-simulation
solar
gravitation
glm
physics-simulation
solarsystem
mfc
shadow
gravitational-simulations
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Nov 18, 2020 - C++
a logistics and persistence engine for the analysis of molecular dynamics trajectories
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Jan 24, 2020 - Python
MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store
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Jan 15, 2021 - HTML
PyRod - Tracing water molecules in molecular dynamics simulations
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Jan 5, 2021 - Python
A python framework to run adaptive Markov state model (MSM) simulation on HPC resources
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Sep 13, 2019 - Python
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Jan 18, 2021 - C++
Full automation of relative protein-ligand binding free energy calculations in GROMACS
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Jan 15, 2021 - Python
Toolkit to aid in the analysis of lipid bilayer molecular simulation trajectories.
molecular-simulation
molecular-dynamics-simulation
analyses
molecular-dynamics-trajectories
lipids
lipid-bilayers
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Sep 17, 2019 - Python
ls1-MarDyn is a massively parallel Molecular Dynamics (MD) code for large systems. Its main target is the simulation of thermodynamics and nanofluidics. ls1-MarDyn is designed with a focus on performance and easy extensibility.
simulation
molecular-dynamics
scientific-computing
molecular-dynamics-simulation
ls1-mardyn
nanofluidics
autopas
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Jan 19, 2021 - C++
Open
Add coverage metrics
HaoZeke
commented
Mar 12, 2020
Is your feature request related to a problem? Please describe.
Currently it is difficult to keep track of which tests are present and which should be implemented.
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- Given that it is a
C++project, it makes sense to uselcov
A repository for tutorials and FAQ's about LigParGen
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Aug 12, 2018 - Python
pKa estimates for proteins using an ensemble approach
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Jul 14, 2020 - Python
A program implementing event driven molecular dynamics for hard smooth spheres, using OpenGL for displaying
opengl
lightning
simulation
shaders
physics
sphere
molecular-dynamics
collision
particles
computational-physics
molecular-dynamics-simulation
event-driven
glm
mfc
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Nov 18, 2020 - C++
Python bindings for TNG file format
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Dec 11, 2020 - C
A python toolkit for analysing membrane protein-lipid interactions.
python
molecular-dynamics
networkx
pymol
molecular-dynamics-simulation
mdtraj
molecular-modeling
molecular-dynamics-analysis
lipid-interactions
koff
pdb-structure
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Jan 11, 2021 - Python
This repository contains the code for simulating the growth of a Biofilm after attachment using Molecular dynamics simulation methods. The project was build as part of the iGEM 2020 Contest. The BiofilmSimulation software can be installed as A python package, documented under https://pypi.org/project/BiofilmSimulation.
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Jan 18, 2021 - Jupyter Notebook
CHAP is a tool for the functional annotation of ion channel structures:
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Apr 30, 2020 - C++
Program that implements assembling and disassembling of microtubules
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Mar 4, 2019 - C++
To analyze fluctuations in DNA or RNA structures in molecular dynamics trajectories.
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Dec 13, 2018 - Python
Python tool to submit several PBS jobs on the HPC
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Nov 6, 2020 - Python
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SENPAI does not yet understand the concept of bond torsion.
As an example, ethylene is supposed to be a planar molecule, but SENPAI will allow unrestricted rotation over the C=C double bond.
