OpenFF 2.3.0rc2 Relative Binding Free Energy Benchmarks

Overview

Relative binding free energy benchmarks of the openff-2.3.0rc2 release using the JACS set from (https://github.com/OpenFreeEnergy/IndustryBenchmarks2024).

Contents

Benchmark variants

The following benchmark variants were run:  * `openff-2.3.0rc2_elf10`: simulations using OpenFF 2.3.0rc2 and AM1BCCELF10 charges using the OpenEye Toolkit.  * `openff-2.3.0rc2_nagl`: simulations using OpenFF 2.3.0rc2 and AshGC v0.1rc3 charges

For additional validation, an extra 3 replica were run for both variants across all sets. Results have been collated in separatefiles which are labelled with the tag `6replica` in their name.

RBFE data

The `data` folder contains all the ddG data for each transformation in each set.

Per system data files

These are stored as TSV files within subdirectories for each system in the JACS set.Reference CSV data (labelled as `{system}_ref.csv`), taken from the Ross et al. 2023 dataset (https://github.com/schrodinger/public_binding_free_energy_benchmark)can also be found.

Aggregate dG and ddG files

CSV files with all the dG and ddG values for all datasets can be found in `data`.

Simulation details

* All simulations were carried out using the RelativeHybridTopology protocol in OpenFE v1.4.* Mappings were created using Kartograf, these are the same as those used in the OpenFE industry benchmarks.* Transformation edges were created using Lomap, these are the same as those used in the OpenFE industry benchmarks.* Simulations used openfe default settings, except the following:  * Dodecahedron solvent box with 1 nm padding in complex and 1.5 nm padding in solvent  * 2.5 ps HREX exchange rate  * 0.9 nm short range interaction cutoff  * 3 replica were originally run, and then a further 3 were added to the `6replica` files.

概述
本数据集为OpenFF 2.3.0rc2版本的相对结合自由能（Relative Binding Free Energy, RBFE）基准测试集，采用了来自https://github.com/OpenFreeEnergy/IndustryBenchmarks2024的JACS基准集。

数据集内容
基准测试变体
本次运行的基准测试变体如下：
* `openff-2.3.0rc2_elf10`：使用OpenFF 2.3.0rc2力场与通过OpenEye Toolkit生成的AM1BCCELF10电荷完成模拟。
* `openff-2.3.0rc2_nagl`：使用OpenFF 2.3.0rc2力场与AshGC v0.1rc3电荷完成模拟。

为开展额外验证，针对所有基准集的上述两种变体均额外运行了3组重复模拟。所有结果已整理至文件名带有`6replica`标签的独立文件中。

相对结合自由能数据
`data`文件夹包含了各基准集中每个转化过程的全部ddG（相对结合自由能差值）数据。

单体系数据文件
此类文件以TSV（制表符分隔值，Tab-Separated Values）格式存储于JACS基准集各对应体系的子目录内。同时还可获取参考CSV（逗号分隔值，Comma-Separated Values）数据，其命名格式为`{system}_ref.csv`，该数据取自Ross等人2023年发布的基准数据集（https://github.com/schrodinger/public_binding_free_energy_benchmark）。

聚合dG与ddG文件
包含所有数据集的全部dG（结合自由能）与ddG（相对结合自由能差值）值的CSV文件可在`data`目录中获取。

模拟细节
* 所有模拟均通过OpenFE v1.4中的RelativeHybridTopology协议完成。
* 分子拓扑映射通过Kartograf工具生成，与OpenFE行业基准测试中使用的映射完全一致。
* 转化边通过Lomap工具构建，与OpenFE行业基准测试中使用的转化边完全一致。
* 模拟默认采用OpenFE标准设置，仅对以下参数进行了调整：
* 采用十二面体溶剂盒，复合物体系的溶剂填充间距为1 nm，纯溶剂体系为1.5 nm
* HREX（哈密顿副本交换）交换速率为2.5 ps
* 短程相互作用截断距离为0.9 nm
* 初始运行3组重复模拟，随后新增3组重复以生成带有`6replica`标签的数据集文件。