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Open Access Publication in the Spotlight (October) - 'Q-Force: Quantum Mechanically Augmented Molecular Force Fields'

Date:25 October 2021
Author:Open Access Team
Open access publication in the spotlight: October 2021
Open access publication in the spotlight: October 2021

Each month, the open access team of the University of Groningen Library (UB) puts a recent open access article by UG authors in the spotlight. This publication is highlighted via social media and the library’s newsletter and website.

The article in the spotlight for the month of October 2021 is titled Q-Force: Quantum Mechanically Augmented Molecular Force Fields, written by Selim Sami, Maximilian Menger, Shirin Faraji, Ria Broer and Remco Havenith (all from the Faculty of Science and Engineering).

Abstract

The quality of molecular dynamics simulations strongly depends on the accuracy of the underlying force fields (FFs) that determine all intra- and intermolecular interactions of the system. Commonly, transferable FF parameters are determined based on a representative set of small molecules. However, such an approach sacrifices accuracy in favor of generality. In this work, an open-source and automated toolkit named Q-Force is presented, which augments these transferable FFs with molecule-specific bonded parameters and atomic charges that are derived from quantum mechanical (QM) calculations. The molecular fragmentation procedure allows treatment of large molecules (>200 atoms) with a low computational cost. The generated Q-Force FFs can be used at the same computational cost as transferable FFs, but with improved accuracy: We demonstrate this for the vibrational properties on a set of small molecules and for the potential energy surface on a complex molecule (186 atoms) with photovoltaic applications. Overall, the accuracy, user-friendliness, and minimal computational overhead of the Q-Force protocol make it widely applicable for atomistic molecular dynamics simulations.

We asked first and corresponding author Selim Sami a few questions about the article:

This article was published open access, was open access a deliberate choice?

Yes, it was. Publicly funded research should be accessible to the public. Moreover, with the facilities that UG provides for publishing open access, we do not have to go out of our way to do so: The agreements with the publishing houses make it cost-free for the individual researcher and the streamlined process makes it completely effortless. Finally, it is also beneficial for us to have our research more accessible and visible.

Your research was sponsored by NWO. Did requirements of the funder play a role in your choice to publish open access?

It is indeed a requirement by NWO to publish open access. However, were it not so, we would have still published open access due to the points I have made above. I think that UG and the Netherlands as a whole have done a great job in not only promoting but also facilitating open access publications.

This article is about Q-Force, an open source toolkit that you and your colleagues developed. Why did you decide to make the toolkit openly available?

We wanted Q-Force to be accessible to the community so that they can use it, review it and perhaps even make their own contribution to it. Personally, I have always found open source code more inviting. I don’t want to say trustful, because open source actually takes trust out of the equation. I think that if you cannot view a newly written code  (i.e., not extensively tested), you cannot reliably use it!

Is the use of open source applications common in your field?

It is definitely becoming increasingly common. I notice that especially the new generation of scientists are very motivated to share their code open source in Git repositories. It used to be quite common to say: “the executable for the software can be requested from the authors, free of charge”. Nowadays, if I see such a paper or software, I avoid it. Again, if you cannot view the code, you cannot reliably use it!

Did you receive any support or guidance from the university in making Q-Force available as an open source toolkit? In your view, is there a need for support or guidance on this topic at our university? 

We have neither requested nor received individual support from UG for making Q-Force open source. This is quite a straightforward process so I think that there is no need for individual support. Perhaps Center for Information Technology (CIT) could organize courses on open source programming collaborations using Git repositories .

Could you reflect on your experiences with open access and open science in general?

My experience is that open science promotes collaborations. Our work on Q-Force was published only about 3 months ago and already a group from Sweden has implemented new features into Q-Force that were important for their own research and a group from the UK interfaced Q-Force into their own software. This would not have happened, at least not at a comparable speed, if Q-Force was not open source.

This forceful article was a real tour de force! Was the Force with you when you wrote this article? Could you feel the force?

"I am one with the Q-Force and the Q-Force is with me".  In reality though, when I came up with the name, I had more X-Force from Marvel in mind rather than Star Wars. And now there is a Netflix series called Q-Force, so there really is no end to the pop-culture references in this project.

Useful links:

A Git repository tracks and saves the history of all changes made to the files in a Git project. Some popular git repositories are GitHub, SourceForge, Bitbucket and GitLab.

Funder policies: Most research funding organizations require publications resulting from publicly funded grants to be published open access. Most funders allow article processing charges to be paid from grant money, although conditions apply. See this support page for more information about funder policies.

Open access journal browser: search engine that can be used to check if a discount on the article processing charge (APC) is available for a specific journal. UG corresponding authors can publish with an APC discount (mostly 100%, so for free) in more than 12.000 journals! 

The Open Science Community Groningen facilitates open science practices through workshops, lectures and materiels on their website.

Citation:

Sami, S., Menger, M. F. S. ., Faraji, S., Broer, R., & Havenith, R. W. A. (2021). Q-Force: Quantum Mechanically Augmented Molecular Force Fields. Journal of Chemical Theory and Computation, 17(8), 4946–4960. doi:10.1021/acs.jctc.1c00195 

If you would like us to highlight your open access publication here, please get in touch with us.

About the author

Open Access Team
The Open Access team of the University of Groningen Library

Link: /openaccess
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