From 39efcea5d8001fd46e7af5b61c5501bc996b5592 Mon Sep 17 00:00:00 2001 From: chrisjonesbsu Date: Mon, 13 Nov 2023 08:52:09 -0700 Subject: [PATCH] fix 2 spelling typos, and correct hoomd citaiton --- paper/paper.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index 85abc4a7..b78048d1 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -30,13 +30,13 @@ date: 16 October 2023 bibliography: paper.bib --- # Summary -`flowerMD` is a package for reproducibly performing multi-stage HOOMD-blue [@hoomd_2019] +`flowerMD` is a package for reproducibly performing multi-stage HOOMD-blue [@anderson2020hoomd] simulation workflows. It enables the programmatic specification of tasks including definition of molecular structures, forcefield definition and application and chaining together simulation stages (e.g., shrinking, equilibration, simulating a sequence of ensembles, tensile testing, etc.) through an extensible set of Python classes. The modular design supports a library of workflows for organic -macrmolecular and polymer simulations. Tutorials are provided to demonstrate +macromolecular and polymer simulations. Tutorials are provided to demonstrate package features and flexibility. @@ -51,14 +51,14 @@ to be validated and extended. Lowering the cognitive load of performing molecular simulations helps computational researchers of all levels of expertise reason about the logic of a simulation study. This is particularly important for researchers new to -the discipline becuase developing the tools needed to perform experiments often +the discipline because developing the tools needed to perform experiments often involves: (a) gaining new software development skills and knowledge, and (b) repeating work that others have already performed. Recent advances in open-source tools have made the programmatic specification of molecular simulation components easier than ever -[@hoomd_2019; @lammps_2022; @eastman2017openmm; @Klein2016mBuild; @gmso; @parmed; +[@anderson2020hoomd; @lammps_2022; @eastman2017openmm; @Klein2016mBuild; @gmso; @parmed; @Santana-Bonilla_2023; @polyply_2022; @biosimspace_2019; @martin2018pyprism]. Individually, each of these tools lower the cognitive load of one aspect of an overall workflow such as representing molecules, building initial structures,