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daico007 committed Feb 1, 2024
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Expand Up @@ -95,7 +95,7 @@ The General Molecular Simulation Object, or GMSO, is an open-source Python packa

# Statement of need

The General Molecular Simulation Object (GMSO) is a component of the Molecular Simulation Design Framework (MoSDeF), provides a framework and utilities for storing, manipulating, and outputting of molecular systems. The Molecular Simulation Design Framework (MoSDeF) is a suite of software tailored to facilitate the initialization of chemical and biomolecular systems for computational simulations [@cummings2021opena]. These tools were developed to specifically address a critical aspect of the (ir)reproducibility issue within the molecular simulation community — namely, the insufficient documentation of the structure preparation process and force field parameter implementation [@thompson2020towards]. The initialization step, often performed through Graphical User Interfaces (GUI) or via the use of ad-hoc, unpublished, and unreviewed code, poses the risk of introducing irreproducible and untraceable errors[@baker2016reproducibility]. By providing general-purposed and standardized tools that build and parameterize molecular systems for molecular simulations, directly support various molecular dynamics (MD) and Monte Carlo (MC) engines, MoSDeF aims to trivialize the describing and disseminating such processes without creating extra burdens for computational simulation researchers [@cummings2021opena].
The General Molecular Simulation Object (GMSO) is a component of the Molecular Simulation Design Framework (MoSDeF), provides a framework and utilities for storing, manipulating, and outputting of molecular systems. MoSDeF is a suite of software tailored to facilitate the initialization of chemical and biomolecular systems for computational simulations [@cummings2021opena]. These tools were developed to specifically address a critical aspect of the (ir)reproducibility issue within the molecular simulation community — namely, the insufficient documentation of the structure preparation process and force field parameter implementation [@thompson2020towards]. The initialization step, often performed through Graphical User Interfaces (GUI) or via the use of ad-hoc, unpublished, and unreviewed code, poses the risk of introducing irreproducible and untraceable errors[@baker2016reproducibility]. By providing general-purposed and standardized tools that build and parameterize molecular systems for molecular simulations, directly support various molecular dynamics and Monte Carlo engines, MoSDeF aims to trivialize the describing and disseminating such processes without creating extra burdens for computational simulation researchers [@cummings2021opena].


The initialization of chemical/biomolecular systems comprises of three key steps:
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