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183 search results found

Teaching Utility for Classical Atomistic Simulation.

Clusttraj ⭐ 16

Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.

Nmrformd ⭐ 16

NMRforMD is a python script for the calculation of NMR relaxation time T1 and T2 from molecular dynamics trajectory file.

Openmm Tutorials ⭐ 15

Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM

Pygromostools ⭐ 15

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

Adaptivepele ⭐ 14

AdaptivePELE is a Python package aimed at enhancing the sampling of molecular simulations

Dockingml ⭐ 14

A package for MD, Docking and Machine learning drug discovery pipeline

Mastermsm ⭐ 14

Python package for generating Markov state models

Command line interface for MDAnalysis

Lindemann ⭐ 13

lindemann is a python package to calculate the Lindemann index of a lammps trajectory

A Python Package to Automate Thermodynamic Integration Calculations for Free Energy

Schrodinger_utils ⭐ 12

Various integrations to the Schrodinger ecosystem. With major interest on analysis tools for Molecular Dynamics simulations run with Desmond.

Sarkas Python MD suite for Dense Plasmas Physics

Md Alaninedipeptide ⭐ 11

Molecular Dynamics Simulation of Alanine Dipeptide and Dihedral Angle Analysis

Mastermsm ⭐ 11

Python package for generating Markov state models

Molsysmt ⭐ 11

Open source library to work with molecular systems

Polymer_metal_interface ⭐ 11

Provides some useful information and the LAMMPS input files to model a polymer-metal interface.

Lintools ⭐ 11

Python script that creates 2D protein-ligand interaction images

Partycls ⭐ 11

Unsupervised learning of structure in systems of interacting particles.

Analysis of contacts in molecular dynamics trajectories

A package for managing pair-potential derivation using MultiState Iterative Boltzmann Inversion (MS-IBI)

Mdanalysisdata ⭐ 10

Access to data for workshops and extended tests of MDAnalysis.

Python package for working with multiscale simulation data.

Accelerated_sampling_with_autoencoder ⭐ 10

Accelerated sampling framework with autoencoder-based method

Paratemp ⭐ 10

A package for molecular dynamics analysis and parallel tempering in GROMACS

Mode Task ⭐ 10

PCA and normal mode analysis of proteins

Molecular dynamics by NMR data analysis (mirror of the relax repository)

Codebase of the paper "Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling" (ICLR 2024)

Mdstudio ⭐ 10

A general framework for microservice based distributed applications

Pydiffusion ⭐ 10

Analyse Rotational Diffusion Tensor from MD Simulations

SAPT energy calculator built using MDAnalysis and Psi4

Differentiable Markov Chain Monte Carlo

Alchemtest ⭐ 9

the simple alchemistry test set

Mosdef Workflows ⭐ 9

Sample molecular simulation workflows using a MoSDeF and community tools

Cadishi: CAlculation of DIStance HIstograms

This python code creates hybrid MD/MC (NAMD/GOMC) simulations for the NVT, NPT, GCMC, and GEMC-NVT ensembles

Python tools for VMD

Ensemble_md ⭐ 9

A python package for performing GROMACS simulation ensembles

Python toolkit for molecular dynamics analysis

MD DaVis: A python package to analyze molecular dynamics trajectories of proteins

Create, use, and analyze machine learning potentials within the many-body expansion framework.

Molecular dynamics package designed for the SIESTA DFT code.

Mmelemental ⭐ 8

Python implementation of the MMSchema specification. Provides fundamental models for molecular mechanics.

Simphony Lammps ⭐ 8

The LAMMPS engine-wrapper for the SimPhoNy framework

Pymembrane ⭐ 8

Advanced Coarse-Grained Membrane Simulation

Scripts to prepare and analyze molecular dynamics simulations

Polarisable force field for ionic liquids

asyncmd is a library to write concurrent code for setup, run and analysis of molecular dynamics simulations using pythons async/await synthax.

Neural network class for molecular dynamics to predict potential energy, forces and non-adiabatic couplings.

Smartsim Openmm ⭐ 7

SmartSim used to implement the DeepDriveMD workflow with OpenMM

Maxentvampnet ⭐ 7

Repository for Maximum Entropy VAMPNet Adaptive Sampling

Unsupervised landmark analysis for jump detection in molecular dynamics simulations.

CLI toolkit for training and applying DeePMD models

Gromacstutorials.github.io ⭐ 7

Repository of the gromacstutorials webpage

Read and write H5MD files

Fast clustering of long Molecular Dynamics

Useful Collective Variables for OpenMM

QM/DMD engine. Protein Hybrid Discrete Dynamics/DFT

Smartsim Lammps ⭐ 6

Examples of running LAMMPS with SmartSim

Demystifying ⭐ 6

molecular dynamics, with Fireworks!

MDMS: Molecular Dynamics Made Simple; Python program facilitating performing Molecular Dynamics simulations of proteins

Remd_analysis ⭐ 6

A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations

Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.

Md Tracks ⭐ 6

MD-Tracks is a statistical analysis toolkit for molecular dynamics and monte carlo simulations.

Multi Ego ⭐ 5

Set of tools to generate a multi-eGO force field to perform molecular dynamics simulations

Spica Tools ⭐ 5

Tools for coarse-grained molecular dynamics simulations using the SPICA force field

Moleculearn ⭐ 5

Extract patterns from ab-initio molecular dynamics simulations using machine learning.

Prolint2 is an optimized tool for analyzing and visualizing lipid-protein interactions from molecular dynamics trajectories.

Thresholds ⭐ 5

Utilities for determining maximum tolerable timesteps. See https://doi.org/10.3390/e20050318

ConfID: an analytical method for conformational characterization of small molecules using molecular dynamics trajectories

🚰A tool to characterize the local structure of liquid water by geometric order parameters.

Plumed Pybias ⭐ 5

PyBias: PLUMED plug-in with embeded Python

Forcefield_template ⭐ 5

A template repo for disseminating force fields with foyer

Peptidesim ⭐ 5

Automated peptide simulation tool with gromacs, gromacswrapper, plumed

The Energy Expression Exchange for Molecular Dynamics.

Python-based library for easy force-field fitting

MicMec, the first implementation of the micromechanical model, ever.

Este repositorio debe ser el punto de partida y encuentro para cualquier investigador o estudiante que quiera comenzar a trabajar con/en la UIBCDF. Si has caído aquí por otro motivo y este material te es útil, eres más que bienvenido a usarlo e interaccionar con nosotros.

Pyxmolpp2 ⭐ 5

Processing and analysis of MD trajectories

History-augmented Markov analysis of weighted ensemble trajectories.

Tools for running MD simulations in OpenMM

Mdproptools ⭐ 5

A Python package for LAMMPS analysis tools

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