Centre for Computational Science (UCL)

EasyVVUQ

Python 3 framework to facilitate verification, validation and uncertainty quantification (VVUQ) for a wide variety of simulations.

symmer

An efficient Python-based framework for implementing qubit subspace methods, reducing the resource requirements for near-term quantum simulations.

TIES_MD

Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.

SCEMa

HMM implementation featuring Deal.II (FE) and LAMMPS (MD)

FabSim

Superseded by FabSim3.

HemePure

HemeLB version with improved memory, compilation and scaling

Nbed

Python package to reduce the qubit requirements of quantum simulation by embedding into DFT.

HemePure-GPU

GPU version of HemeLB code (HemePure)

TIES

Topology Superimposition based on joint graph traversal

BAC2

A tool for the automation of molecular simulations using multiple engines, focusing on binding affinity calculations

FabNEPTUNE

FabNEPTUNE is a FabSim3 plugin for automated NEPTUNE (UKAEA’s fusion project)-based simulations

PINN-WM-LBM

QuantumTools

Random useful quantum computing for chemistry things.

bac-docker

FabMD

FabMD is a FabSim3 plugin for automated LAMMPS-based simulations.

FabSCEMa

FabSCEMa is a FabSim3 plugin for automated SCEMa-based simulations.

hemeXtract

Reads and analyses HemeLB .xtr output files

LargeScaleTIES

UQ_NAMD

High-dimension parameters sensitivity analysis of binding affinity simulations with NAMD using EasyVVUQ and EasyPJ

brd4-diverse-esmacs

Data from the paper "Application of ESMACS binding free energy protocols to diverse ligand datasets:Bromodomain-containing protein 4"

DRTNN

Deep Residual Transformer Neural Network (DRTNN)

esmacs-input-creation-docs

Description of methods to create BAC compatible protein-ligand system descriptions for ESMACS simulations

HemeLBData_FistulaInputs50um

HemeLB input data for 50um resolution arteriovenous fistula study

HemePure_SelfCoupled

Self-coupled version of HemeLB

HemePure_tools

ldha-diverse-esmacs

Data from the paper "Application of ESMACS binding free energy protocols to diverse ligand datasets: lactate dehydogenase A"

LongTimescaleStudy

Data associated with the long timescale study.

ML-PB-Covid-drug

ParmEd

Parameter/topology editor and molecular simulator

uclrpn-web

The website of the UCL Research Programming Hub