GitHub topics: molecular-simulation

Repositories

mindleaving/genome-tools

Tools for exploration and analysis of biochemical data like genomics and proteins

Language: C# - Size: 905 KB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 2

VlachosGroup/Pdn-CO-Dynamics

Lattice Kinetic Monte Carlo (KMC) Simulations for Subnanometer Pdn clusters Dynamics under a pressure of CO.

Language: Python - Size: 765 MB - Last synced at: 3 months ago - Pushed at: about 4 years ago - Stars: 6 - Forks: 1

Ferg-Lab/integrin_molgen

Deep generative modeling of large multi-molecular systems

Language: Jupyter Notebook - Size: 313 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

lexin-chen/SciArt

aesthetic 3D images of biomolecules on Blender

Language: Tcl - Size: 34.3 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

aiqm/aimnet

Atoms In Molecules Neural Network Potential

Language: Python - Size: 19 MB - Last synced at: almost 2 years ago - Pushed at: almost 6 years ago - Stars: 77 - Forks: 23

ekaakurniawan/hppNeuroDock

Molecular Docking Simulation Tool

Language: Python - Size: 34.6 MB - Last synced at: almost 2 years ago - Pushed at: about 8 years ago - Stars: 3 - Forks: 3

nkkchem/CompMolNWChem

Language: Python - Size: 1.69 MB - Last synced at: almost 2 years ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 2

qusers/Q6

Q6 Repository -- EVB, FEP and LIE simulator.

Language: Fortran - Size: 33.9 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 30 - Forks: 16

lopesth/MoleKing_util

MoleKing_util is a Python module written in C++ with pybind11. This module contains several useful classes for those who program python scripts aimed at theoretical chemistry.

Language: C++ - Size: 1.5 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

mcolahan/mole-sim

Code for my PhD level molecular simulations class at Ohio University (CHE 7120)

Language: Jupyter Notebook - Size: 32.9 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0

juexinwang/NRI-MD

Neural relational inference for molecular dynamics simulations

Language: Python - Size: 13.1 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 26 - Forks: 12

Ferg-Lab/pines

Permutationally invariant networks for enhanced sampling (PINES)

Language: C++ - Size: 26.3 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

dquigley533/mc_water_ls_mw

Lattice-Switching Monte Carlo Code for the mW water model

Language: Fortran - Size: 215 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 2

ninjab3381/nmr_glycerol

Study of molecular motion of Glycerol using NMR modeling and simulations

Language: Python - Size: 32.3 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

kohnakagawa/LSCMD

A local stress calculation library for molecular dynamics simulations written in C++11

Language: C++ - Size: 57.6 KB - Last synced at: about 2 years ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0

lyczak/MolecularPreloader 📦

📉 A 2D Maxwell Boltzmann distribution generator.

Language: F# - Size: 14.5 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

smlee99/InteractionGroup

Energy decomposition module for the analysis of molecular dynamics trajectories

Language: Python - Size: 434 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0

Vikasdubey0551/svd_angle_between_vectors

'Fits' a vector/vectors to the helix/helicies using Singular Value Decomposition (SVD) and measures angle between them in a trajectory.

Language: Python - Size: 23.4 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0

achattaraj/maximal_Solubility_product

Python scripts to analyze and visualize the data presented in the research article: "The maximum solubility product marks the threshold for condensation of multivalent biomolecules".

Language: Jupyter Notebook - Size: 242 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

jmbr/go-replicants 📦

Molecular simulator for proteins that uses Go-type potentials

Language: C - Size: 278 KB - Last synced at: over 2 years ago - Pushed at: about 14 years ago - Stars: 3 - Forks: 1

JaydevSR/ReplicaExchangeMD.jl

Replica Exchange Molecular Dynamics (GSoC 2022 Project)

Language: Julia - Size: 15.9 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 3 - Forks: 0

Open-Science-Community-Saudi-Arabia/moleculardymics

This workflow for molecular dynamics simulation of proteins

Language: Groovy - Size: 2.16 MB - Last synced at: 5 days ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 2

openmm/openmm-tensorrt

OpenMM plugin to define forces with a TensorRT graph

Language: C++ - Size: 137 KB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 6 - Forks: 2

ThatPerson/MOLEC 📦

Language: C - Size: 28.3 KB - Last synced at: 9 months ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

MolBioMedUAB/RCBS.py

RCBS.py (Reactivity of Chemical and Biochemical Systems) is a Python package that contains several scripts, functions and classes that simplify the analysis of chemical and biochemical simulations.

Language: Python - Size: 9.33 MB - Last synced at: 3 days ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

Inniag/openmm-scripts-amoeba

:microscope: OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field

Language: Python - Size: 190 KB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 15 - Forks: 4

austin-mroz/SMORES

Calculation of electric-field-based steric (Sterimol) parameters.

Language: Python - Size: 4.2 MB - Last synced at: 5 months ago - Pushed at: almost 2 years ago - Stars: 4 - Forks: 1

TomMakesThings/Gillespie-mRNA-Simulator

An mRNA reaction scheme simulator using the Doob-Gillespie algorithm in R

Language: HTML - Size: 15.8 MB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

dejac001/GEMC_histogram_analysis

An analysis package utilizing histograms to calculate accurate vapor and liquid coexistence densities, saturated vapor pressure, and compressibility factor from a Gibbs ensemble Monte Carlo trajectory for unary vapor--liquid equilibria near the critical point.

Language: Python - Size: 629 MB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 6 - Forks: 1

fabianmcg/vina-mpi

Vina MPI is a MPI ready version of the docking software Autodock Vina.

Language: C++ - Size: 133 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

marinadunn/covid19-drug-screening-ML

Developed as part of the Lawrence Livermore National Laboratory Data Science Summer Institute 2022 Challenge Problem. Screening molecular inhibitors for SARS-CoV-2 protein targets with Deep Learning Models.

Language: Jupyter Notebook - Size: 29.6 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

GaillacR/PhD_scripts

MD outputs analysis, CRYSTAL14 output handling

Language: Python - Size: 134 KB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 3 - Forks: 1

RoyRangarirai/chemistry-lab

Welcome to the Lab! Let's Advance the chemical sciences with molecular simulations. 🧪

Size: 0 Bytes - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

satendrapandeymp/nnair

This Repo will contain Assignments and Project for course Molecular dynamics and simulations.

Language: C++ - Size: 27.3 MB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

HammerSeb/xDimer

Simulation of multi-molecular emission spectra dominated by intermolecular vibrations

Language: Python - Size: 63.5 KB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

LucaCaivano/CompTech4MolMod Fork of ManfredNesti/CompTech4MolMod

Projects of the numerical part of the course Computational Techniques for Molecular Modeling. Simulations on molecular modelling and molecular dynamics.

Size: 787 MB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

MDSYN2019/Research

PhD Molecular Dynamics Analysis Code - updated daily

Language: Roff - Size: 57.9 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

sunsistemo/interactiveMD

Seminars Computational Science 2016, University of Amsterdam. Slides for the presentation on the paper "Interactive Molecular Dynamics" by professor Daniel V. Schroeder

Language: JavaScript - Size: 2.19 MB - Last synced at: over 2 years ago - Pushed at: over 9 years ago - Stars: 1 - Forks: 0

nlesc-nano/flamingo

Computation and filtering of molecular properties

Language: Python - Size: 15.2 MB - Last synced at: 3 days ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

ElsevierSoftwareX/SOFTX-D-21-00140 Fork of danjodc/OpenMechanochem

This module includes functions that can be used to simulate mechanochemical phenomena. To cite this Original Software Publication: https://www.sciencedirect.com/science/article/pii/S2352711021001436

Size: 186 KB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0