Irfan Alibay's Projects
a high-throughput alchemical free energy execution system for use with HPC, cloud, bare metal, and Folding@Home
Utility scripts for handling submissions, analysis of alchemical transformations using Alchemiscale
the simple alchemistry library
Code and resources for the EPSRC BioSimSpace project.
Conversion of coarsegrain to atomistic (complete rewrite of the original CG2AT)
MDAnalysis analysis class for checking structure quality
A conda-smithy repository for conda-forge-pinning.
A conda-smithy repository for distopia.
Benchmark set for absolute binding free energy calculations of fragment optimisations
Basic GPU monitoring utility
A repository of Grimoirelab deployment configs for various projects
An MDAKit implementing a Python interface for the HOLE program.
Which schedulers do public facing HPC systems use?
Python script that creates 2D protein-ligand interaction images
A conda-smithy repository for mdahole2.
Toolkit to calculate the surface accessible area of a molecular dynamic trajectory
The MDAnalysis Toolkits Registry
MDAnalysis is a Python library to analyze molecular dynamics trajectories.
A conda-smithy repository for mdanalysis.
A repository for MDAnalysis talks
MDAnalysis home page mdanalysis.org as GitHub pages.
Python code for generating Boresch restraints from MD simulations
OMSF website
A conda-smithy repository for openfe.
A collection of scripts for handling OpenFE in non-standard ways
Working grounds for showcasing OpenFE capabilities
OpenFF NAGL
The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io