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Files used to put BioSimSpace onto the cloud (via Fn functions)
Development version of plumed 2
Best practice document for alchemical free energy calculations going to livecoms journal
Code and resources for the EPSRC BioSimSpace project.
Files needed to configure the BioSimSpace website and associated Jupyter notebooks on Kubernetes
Sire Molecular Simulations Framework
Unit tests for the BioSimSpace repository.
Script to compute orientational spectral density functions from MD derived autocorrelation functions
Collection of script to facilitate the setup and analysis of simulations performed with the JEDI collective variable
This repository contains scripts and relevant data used for the analysis of the ACK_1 dataset using alchemical free energy methods.
This repository contains input files necessary to reproduce the results from the group submitted to the SAMPL6 competition
A pipeline project for understanding and predict secondary structure of stapled peptides using REMD
Software for automated processing of alchemical free energy calculations
Collection of scripts and protocols to setup, execute and analyse a batch of free energy calculations with somd-freenrg
Contains all input files associated with the lab publication on binding free energies of fragments for Cyclophilin A
Custom scripts to test use of paramfit
Repository containing all of the Sire test data
Sire scripts to post-process a trajectory and perform per-residue interaction energy decomposition analysis
D3R grand challenge input data for alchemical free energy simulations