fjclark
PhD student @michellab developing methods for alchemical free energy calculations.
The University of EdinburghEdinburgh
Pinned Repositories
.dotfiles
Personal dotfiles
a3fe
Automated Adaptive Absolute alchemical Free Energy calculator
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
ani_mmml_corrections
Scripts for carrying out mm->ml corrections with ANI
automated_abfe_analysis
Analysis of automated ABFE calculations run with EnsEquil.
k2dg
A command line tool for converting between dissociation constants and free energies
maize-biosimspace
BioSimSpace nodes for Maize
red
Robust Equilibration Detection
squid
SQUeue Interactive Display
fjclark's Repositories
fjclark/maize-biosimspace
BioSimSpace nodes for Maize
fjclark/red
Robust Equilibration Detection
fjclark/a3fe
Automated Adaptive Absolute alchemical Free Energy calculator
fjclark/ani_mmml_corrections
Scripts for carrying out mm->ml corrections with ANI
fjclark/k2dg
A command line tool for converting between dissociation constants and free energies
fjclark/.dotfiles
Personal dotfiles
fjclark/abfe_analysis
A package for analysis ABFE calculations performed with SOMD.
fjclark/alchemical-best-practices
Best practice document for alchemical free energy calculations going to livecoms journal
fjclark/automated_abfe_analysis
Analysis of automated ABFE calculations run with EnsEquil.
fjclark/BioSimSpace
Code and resources for the EPSRC BioSimSpace project.
fjclark/squid
SQUeue Interactive Display
fjclark/biosimspace-openbiosim
An interoperable Python framework for biomolecular simulation.
fjclark/biosimspace_tutorials_openbiosim
A tutorials suite for BioSimSpace.
fjclark/BioSimSpaceTutorials
fjclark/bss_multiple_distance_restraints_example
Example scripts and inputs for running an ABFE calculation with multiple distance restraints through BioSimSpace
fjclark/cluster_watcher
Script to monitor GPU failuers on the cluster
fjclark/coding-retreat2022
Progress from the OpenMM-MACE hackathon
fjclark/file_store
Files which I need to be able to access via the internet.
fjclark/fjclark
My personal repository.
fjclark/k2dg_streamlit_app
A streamlit app to interconvert free energies of binding and dissociation constants.
fjclark/maize-contrib
Contributed and additional nodes for maize
fjclark/openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
fjclark/rbfe_code_anna
various scripts and code
fjclark/scientific-posters
A selection of my scientific posters.
fjclark/Sire
Sire Molecular Simulations Framework
fjclark/sire-openbiosim
Sire Molecular Simulations Framework
fjclark/sire_website
Repository used to build and host the sire website
fjclark/SireUnitTests
fjclark/somd2
SOMD2 molecular dynamics for free energy calculations
fjclark/somd_abfe_example
Example inputs for an ABFE calculation in SOMD using Boresch restraints