Finlay Clark's repositories
maize-biosimspace
BioSimSpace nodes for Maize
ani_mmml_corrections
Scripts for carrying out mm->ml corrections with ANI
.dotfiles
Personal dotfiles
abfe_analysis
A package for analysis ABFE calculations performed with SOMD.
alchemical-best-practices
Best practice document for alchemical free energy calculations going to livecoms journal
automated_abfe_analysis
Analysis of automated ABFE calculations run with EnsEquil.
BioSimSpace
Code and resources for the EPSRC BioSimSpace project.
squid
SQUeue Interactive Display
biosimspace-openbiosim
An interoperable Python framework for biomolecular simulation.
biosimspace_tutorials_openbiosim
A tutorials suite for BioSimSpace.
bss_multiple_distance_restraints_example
Example scripts and inputs for running an ABFE calculation with multiple distance restraints through BioSimSpace
cluster_watcher
Script to monitor GPU failuers on the cluster
coding-retreat2022
Progress from the OpenMM-MACE hackathon
file_store
Files which I need to be able to access via the internet.
fjclark
My personal repository.
k2dg_streamlit_app
A streamlit app to interconvert free energies of binding and dissociation constants.
maize-contrib
Contributed and additional nodes for maize
openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
rbfe_code_anna
various scripts and code
scientific-posters
A selection of my scientific posters.
Sire
Sire Molecular Simulations Framework
sire-openbiosim
Sire Molecular Simulations Framework
sire_website
Repository used to build and host the sire website
somd2
SOMD2 molecular dynamics for free energy calculations
somd_abfe_example
Example inputs for an ABFE calculation in SOMD using Boresch restraints