michellab

SOMD-tutorials

sire_edecomp

Sire scripts to post-process a trajectory and perform per-residue interaction energy decomposition analysis

spectraldensity

Script to compute orientational spectral density functions from MD derived autocorrelation functions

BioMolSetupPaper

CypAcatalysis_input

Sire-SAMPL5

SAMPL5 challenge data

somdfreenrgbatch

Collection of scripts and protocols to setup, execute and analyse a batch of free energy calculations with somd-freenrg

Stapled_peptides_scripts

Set of various scripts which might (or not) be reusable directly

cypa_datasets

ACK1_Data

This repository contains scripts and relevant data used for the analysis of the ACK_1 dataset using alchemical free energy methods.

Benchmark

A selection of scripts to run Sire and openMM benchmarks on the same datasets

brahan_utilities

CCP-BioSim-Workshop

cutoff-corrections

Set of Sire scripts to correct free energy changes for finite size errors in electrostatic and dispersion interactions

cyp-trivector

cypafragmentsfreeenergy

Contains all input files associated with the lab publication on binding free energies of fragments for Cyclophilin A

D3R_Data

D3R grand challenge input data for alchemical free energy simulations

D3R_GC2_Data

ddGlearn

forcefield_parametrization

jenke_freenrg_utilities

Set of scripts used to automate free energy calculations

Lomap

Alchemical mutation scoring map

paramfit-tests

Custom scripts to test use of paramfit

PME_OpenMM

SAMPL6inputs

This repository contains input files necessary to reproduce the results from the group submitted to the SAMPL6 competition

sireparsertests

Dataset to validate Sire Amber parsers

SireTests

Repository containing all of the Sire test data

sparta