Monday, September 28, 2015

NMRLipids V project: Review about validations of membrane MD simulations

I have been invited by Tomasz Rog and Ilpo Vattulainen to write a review article to a special issue of BBA-Biomembranes about validations of membrane MD simulations. Since the topic is very closely related to the NMRLipids project I asked a permission to use the open collaboration method, introduced in this project, to write also the review. The guest editors and BBA staff supported my suggestion. I was also happy to note that the Elsevier policy contains the sentence "Authors can share their preprint anywhere at any time."

Thus, the writing of this review is now the NMRLipids V project. The deadline for submission is 14th of November 2015.

The focus of the review will be the best data (Order parameters and Spin lattice relaxation from NMR, form factor from scattering) and methods to validate the atomistic resolution structure and dynamics in membrane MD simulations. The focus is not in the details of different models or in actual comparison between force fields (these are discussed in other NMRLipids projects). Also, only structure and dynamics will be covered, not thermodynamics (phase transition temperature, calorimethric data, etc.).

The first draft of the manuscript with (very preliminary) introduction is already in the project GitHub repository. It is straighforward to me to write the NMR part based largely on the content of this project, and also on our recent work. However, I am requesting help especially for the scattering part. There are number of things which are not perfectly clear for me. Many of these issues have been already came up in the discussions related to the NMRLipids III project, thus writing the review will strongly support that project as well.

The recently introduced workflow will be used in this project, i.e. the up-to-date manuscript is all the time in GitHub containing pointers to the more specific issues and related discussion. The best overview of the project status should be obtained by reading the manuscript and the linked issues.

The original rules for the authorship will be applied to the people who comment the blog post containing NMRLipids V in the title or contribute (commit or comment) to the NMRLipids V GitHub repository.

Thus, everyone who has contributed to the project by communicating via this blog or GitHub will be offered coauthorship. The final decision on authorship will be to the invited individuals themselves. They should base their decision on self-assessment of their scientific contribution to the project. The order of all names in the final manuscript will be alphabetical. O.H. Samuli Ollila will be the corresponding author.





5 comments:

  1. The order parameter section text of the review is now close to the final form. All kind of comments from the language to the scientific content and understandability are welcomed. The scattering part is currently progressed through the discussions the GitHub issues and I will work on the dynamics section now.

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  2. The text of the review is now close to the final format. The figures needs polishing yet. The review will be submitted on Friday 20.11.2015. All comments are welcomed.

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  3. In my opinion the manuscript is now in submittable shape. My intention is to submit it tomorrow.

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  4. This is now published in the Journal:
    http://dx.doi.org/10.1016/j.bbamem.2016.01.019

    ReplyDelete
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