diff --git a/joss_paper/paper.md b/joss_paper/paper.md index 7560e844..ea284693 100644 --- a/joss_paper/paper.md +++ b/joss_paper/paper.md @@ -88,7 +88,7 @@ Notably, absolute binding free energy calculations between proteins and ligands The resultant estimates of these free energies are essential for understanding binding affinity throughout various stages of drug discovery, such as hit identification and lead optimization [@merz2010drug]. Other free energies extracted from simulations are useful in solution thermodynamics, chemical engineering, environmental science, and material science [@Schlaich2015aa]. -Molecular simulation packages such as [GROMACS](https://www.gromacs.org/) [@Abraham2015aa], [Amber](https://ambermd.org/) [@Case2005uq], [NAMD](https://www.ks.uiuc.edu/Research/namd/) [@phillips2020scalable], [LAMPPS](https://lammps.org/) [@Thompson2022aa], and [GOMC](https://gomc-wsu.org/) [@Nejahi2021aa] are used to run free energy simulations and many of these packages also contain tools for the subsequent processing of simulation data into free energies. +Molecular simulation packages such as [GROMACS](https://www.gromacs.org/) [@Abraham2015aa], [Amber](https://ambermd.org/) [@Case2005uq], [NAMD](https://www.ks.uiuc.edu/Research/namd/) [@phillips2020scalable], [LAMMPS](https://lammps.org/) [@Thompson2022aa], and [GOMC](https://gomc-wsu.org/) [@Nejahi2021aa] are used to run free energy simulations and many of these packages also contain tools for the subsequent processing of simulation data into free energies. However, there are no standard output formats and analysis tools implement different algorithms for the different stages of the free energy data processing pipeline. Therefore, it is very difficult to analyze data from different simulation packages in a consistent manner. Furthermore, the native analysis tools do not always implement current best practices [@klimovich2015guidelines; @Mey2020aa] or are out of date.