From 533589d0bd3923d55614ea677c1717edc72bbb7b Mon Sep 17 00:00:00 2001 From: finlayclark Date: Mon, 17 Jun 2024 15:30:11 +0100 Subject: [PATCH] Add note explaining input file reequilibration to README --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 73882a4..ccf8088 100644 --- a/README.md +++ b/README.md @@ -50,6 +50,9 @@ print(cost) # In hr/ns ``` You should then modify the `run_adaptive.py` script to match this cost (specifically the `reference_sim_cost` argument to `get_optimal_lam_vals`). +Note that the input files provided are not identical to those used to complete the study, because old input files are incompatible with new versions of Sire due +to an [issue with box vectors](https://github.com/OpenBioSim/sire/issues/49). Hence, the provided equilibrated input files were generated from the original parameterised ligands/ complexes, and the original equilibration steps were repeated. + ## To Reproduce Analyses The `analysis` directory contains the code and inputs required to perform analyses not already performed by `a3fe` by default (when `calc.analyse()` or `calc.analyse_convergence()` is run). Each sub-directory contains two notebooks - "analysis" notebooks use the pre-provided data in the `final_analysis` directories to generate the figures from the paper. These can be run without changes. The "preprocessing" notebooks show examples of the computationally-intensive analyses run on the simulation outputs (not included due to size) to generate the data which which is used in the "analysis" notebooks. These will not work without changes - they are intended to be adapted to run on outputs generated by the user.