Lists (3)
Starred repositories
Weighted Ensemble simulation framework in Python
Fokker-Planck Score Learning: Efficient Free-Energy Estimation under Periodic Boundary Conditions
TS-DAR tutorials. The TS-DAR code is here: https://github.com/xuhuihuang/ts-dar
TS-DAR identifies transition states of protein conformational changes from MD simulations using hyperspherical embeddings in the latent space.
Simulation and Generalized Langevin Equation Study of Lipid Subdiffusion in Biomembrane Phases
Force-field-enhanced Neural Networks optimized library
A program for filling up the missing part of protein structure
PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.
Storehouse for random scripts that may be of some use
The scripts here calculates transverse electron/mass density or neutron SLD for all-atom or Martini membrane systems. The code performs Undulation correction of larger membranes
Operator Forces For Coarse-Grained Molecular Dynamics
Force aggregation code aimed at coarse-grained molecular dynamics
Bayesian Analysis with Python (Second Edition)
Monte Carlo simulated annealing to optimize the CMAP potentials in molecular mechanics force fields with reweighting calculation
A Python module for fast computation of 2D and 3D radial distribution functions (RDFs).
Matbench: Benchmarks for materials science property prediction
Examples of applications of pymbar to various problems in simulation and experiment
Instructions for Building Software on Various Platforms
A Python package to compute and analyze transport properties.
Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
MDAnalysis tool to calculate membrane curvature.
Sample codes for my book on molecular dynamics simulation
A series of self-study lectures on using Python for scientific computing at the graduate level in atomic physics and quantum optics.
ESI for "Accurate estimation of diffusion coefficients and their uncertainties from computer simulation"