A tool for removing atoms in IMD config files, just like a cookie cutter in higher dimensions
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Updated
Dec 9, 2020 - Python
A tool for removing atoms in IMD config files, just like a cookie cutter in higher dimensions
Calculation of electric-field-based steric (Sterimol) parameters.
Open-source, cross-platform application supporting lattice-based kinetic Monte Carlo simulations in crystalline systems
Study of molecular motion of Glycerol using NMR modeling and simulations
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
Simulation of multi-molecular emission spectra dominated by intermolecular vibrations
A library for modular HOOMD-Blue workflows
Plot individual potential functions that comprise force fields. Ideal for presentations. Includes energy terms for bonds (harmonic), angles (harmonic), proper torsion (periodic cosine), improper torsion (harmonic), van der Waals (Lennard-Jones), electrostatics (Coulomb), and the Morse potential.
Analysis postprocessing utilities for my molecular dynamics simulations of LiTFSI-Ether mixtures
'Fits' a vector/vectors to the helix/helicies using Singular Value Decomposition (SVD) and measures angle between them in a trajectory.
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.
Variational Autoencoder (VAE)-based molecular SMILES string generator
Repository for my bachelor thesis and consecutive research on the soliton automata model
Virtual chemistry simulation in 2D based on numpy and numba.
A Python package for extracting and simulating diffuse scattering of X-rays in protein crystals
De novo cyclic protein polypeptide design using reinforcement learning.
Energy decomposition module for the analysis of molecular dynamics trajectories
Codes for automating standard VASP and VASP-related calculations.
automate the setup of atomistic clay models for classical molecular dynamics simulations with GROMACS
MD outputs analysis, CRYSTAL14 output handling
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