Friday, January 16, 2015

Towards first submission to journal

The new version of the first manuscript is now updated to arXiv: I think that the core content of the manuscript is pretty much in its final format already. The current up-to-date version with updated To-Do list can be now found here:

The main issues before submission to a journal are the figures. There have been some discussion that several of them should be clarified, and maybe add some extra figures for clarification as well (Figs. 2, 3 and 6). Also adding some discussion about the results from the force fields which are not among the best three should be considered (ToDo point 20).  The rest of the open issues in ToDo list requires less work. Also proofreading and comments about language would be welcomed.

Anyway, I think that the manuscript is in a state that we should start to consider to which journal we are going to offer it since this slightly affects some writing choices and the style. As always, there are various types of options supported by different arguments. However, due to non-traditional approach used here to produce the results and manuscript, there are more issues to consider than usually.

I have listed here some options and my thoughts about those. Please, express your opinions and suggestions by commenting this post. Ideally, we would reach the consensus. However, if this does not happen, then we will organize a voting.

Different types of options I have thought:

  1. Traditional journal for publications with general interest, e.g. PNAS, JACS, Chemical Science
  2. Traditional journal for publications with general interest in the field, e.g. J. Phys. Chem B, J. Chem. Phys, Phys. Chem. Chem. Phys.
  3. Traditional journal for publications with interest in computational field, e.g. J. Chem. Theor. Comput., J. Comp. Chem.
  4. Modern "open science" journal, e.g. PLOS, Royal Society Open Science.
  5. Historical journal, Philosophical Transaction  

 I have intentionally left out the Elsevier journals since some authors might boycott them.

In addition to the regular issues to be considered when choosing a journal, we have consider also these:

  • Some journals might not accept our manuscript since the content has been already  published (everything is in this blog and in arXiv). To my knowledge this is the first time when this type of work is submitted to a journal (Polymath community seems to publish only in arXiv). Correction: Polymath community has also published in peer reviewed journals.
  • I do not have any money to pay the publication costs. I have not checked the details, but I recall that especially open access journals (e.g. PLOS) is quite expensive, while ACS journals are cheap or even free. The free journals to publish are priority, unless someone wants to pay these costs.
About the regular issues the possible length limitation or limited amount of citations are probably the most important for us (currently we have roughly 12 pages and 152 citations).

I would prefer the first submission to the type 1 journal in the list above, i.e.
journal with publications having general interest. The reason is that I would like to find out if they could publish this kind of work, in principle. This is important question since this might be a barrier for some people to start this kind of collaboration. If the journal rejects our work because it "has been published" already, we know that they are not ready for this yet. If they reject it for some other reason or accept, we know that using the open blog and arXiv publications to generate the publication is not a problem for them. This might encourage people for similar approaches that we are using.


  1. Matti Javanainen has made the text modifications to the manuscript in excellent way. He modified directly the manuscript tex file available in the GitHub and then made a pull request to add a new version of the manuscript into the GitHub repository. In addition, he used latexdiff which can be generated to show the pdf with changes.

    After Matti had added his version I looked the changes through and agreed. Then I changed his version to the up-to-date version and made some minor modifications.

    All the mentioned files can be found from the GitHub repository

    up-to date manuscript

    Version Matti uploaded

    pdf showing the changes made by matti:

    I think that this is a very good and convenient way to work collaboratively with the manuscript. If you want you can also make a pull request directly using the up-to-date manuscript file name (HGmodel_draft3.tex). Then I will accept the pull request, or we will do some discussion before acception. Using latexdiff is very good, but the history will also be saved automatically to the GitHub.

    If you find this difficult (as it may be if you are not familiar with GitHub) you can also send your comments and modifications in some other way. However, keep in mind that it is very important to clearly report somehow what you have done. This is to ease my work to handle the input from large amount of contributors.

  2. [I am posting the following (email) on behalf of a scientist Φ, who wishes to remain anonymous as Φ thinks that the points Φ makes about scientific publishing are controversial enough to possibly cause Φ trouble in the future. I think an anonymous posting is acceptable in this rare case.]

    I happened to see you are preparing to submit the blog-thing for peer review. I have some thoughts on the points you raised, I hope you don't mind me sharing.

    First of all, I myself would not be happy to publish neither on Elsevier nor Springer nor Wiley nor other companies that make piles of money with our work (and with the work of thousands of unpaid reviewers). I should of course include Nature in the list, but Nature is too attractive for most scientists not to be considered.

    Second, regarding the policies on self-archiving (e.g., arXiv) implemented by different publishers:

    1) ACS declares that self-archiving is not allowed at all, neither pre-print nor post-print. The prohibition is explicit. So, no ACS for you guys. (, but you can find it also on the ACS web site).

    2) RSC allows self-archiving in a non-commercial repository (e.g., arXiv), with an embargo period of 12 months. In other words, no pre-prints on arXiv (only post-prints, delayed by 1 year). So no RSC either. (

    3) Open Access. Nice idea, of course, but you need to pay for it. Typically it is very expensive, of the order of $2000. Some offer discounts, though, but those still do not make it cheap.

    In case you don't find money (for Open Access), what is left? Science and PNAS are fine, as far as I understand (source, again, is SHERPA/Romeo). Although, I doubt they will be interested in this particular subject: it is not of general enough interest, in my opinion.

    With this, we have exhausted your list. So you might want to look for other options. For example, a reasonable choice would be the Biophysical Journal, which is fine with self-archiving (and even pre-prints), but it belongs to Elsevier (the entire Cell Press belongs to it). If you don't want to give up principles, the Americal Physical Society and IOP Publishing are both good for your case. Not much else comes to mind.

    Third point, a bit more scientific: On the choice of the field of interest.

    As said, I do not believe this work is of general enough interest to get published in a general-interest journal like Nature, Science, PNAS.

    Some might consider the paper of general interest for a chemist (JACS, Chemical Science) or a physicist (PRL). Excluding the chemical ones (ACS and RSC), you are effectively left with PRL, but I think you would be lucky to see this paper accepted there.

    I think the most likely case is that some specialized journal will consider this. And again, among them, APS and IOP are two good publishers with a few respected journals suitable for you.

    1. Even though ACS journals such as JPC Letters seems to be against preprints (, there seem to be very recent exceptions. Such as the paper from last autumn about the new OPC water model, which was submitted to archive on August 7th and then to JPC Letters on August 22nd and later accepted on October 16th.

      The links to the paper in arXiv and JPC Letters are

      According to Sherpa, JCTC is in the white category, i.e. one "Must obtain written permission from Editor". Here's a blog post from 2012 and according to that the editor of JCTC and JPC A informed that it's fine to submit a paper which has been uploaded to arXiv earlier.

      So I wouldn't give up with JCTC or JPC B which I think are good options for us.

    2. We would like to comment on the second and longest point made by Φ, that is, the scientific publishers' stance on open research.

      It is indeed true that public access to all the scientific content created during a research project (including continuous public access to all the versions of the manuscript) may be a problem, at least following a strict interpretation of the publication policies of many journals.

      However, this (public access to all the scientific content) is one of the core elements that make the open-collaboration approach more effective than the traditional approaches. It is also, we believe, rather probable that public access to all the content increases the impact of the work; furthermore it is advantageous to the whole field to have this access. The efficiency of the open-collaboration approach has now been demonstrated in two distinct fields (Polymath project in mathematics, and our NMRlipids in biophysical chemistry), thus almost certainly there will be more projects like this.

      We believe that the ACS and RSC staff have the wisdom to make correct decisions to keep their journals as the leading communication platforms for the most novel findings in the field of chemistry also in the future.

      For this reason, we would like to let them decide themselves, if our work can be fitted into their publication policy. Whatever their decision, it will be very valuable information for everyone involved, or planning to get involved, in this kind of open-collaboration projects.

      On a personal level, we think that the publication policies of journals should not exclude studies that use the most effective research approaches.

      Samuli Ollila & Markus Miettinen

    3. After thinking these issues for couple of days, I would suggest that we would first submit to JACS or Chemical Science by clearly stating in the cover letter what is behind the work (i.e., continuos open access to all the scientific information through the blog). Thus we will find out if either one of the main chemistry publishers finds our approach acceptable. If they think that the work is not generally interesting enough, but the approach is acceptable, then they probably suggest submission to more specialized journals they publish.

      I would start from chemistry publishers since I think that the scientific content our work is more chemistry than physics.

      Biophysical journal has been mentioned as well. I am not sure about their current policy about publication costs and length limits, but I think we might have problems with both of these.

      PRL is not option for us due to the length of our manuscript.

    4. Interesting discussion. I agree with trying out JACS or Chemical Science first. The novelty of the way this project has been conducted might give us a chance that they go over their "classical" policy.

  3. Here are edits on the preprint ( made directly on the pdf by Luca Monticelli:

    And here a pdf I created; it shows the changes made by Luca:

  4. I have now modified our GitHub repository, such that there is a new folder where the writing happens:

    It contains the manuscript *tex file, figures and bibliography file. Ideally modifications would done by forking the repository and making a pull request. If you are not convenient with GitHub you can send the comments etc. also by some other way. However, it is important to clearly state the changes you have made. If you modify directly the tex file and send it to me, it should be fine since when I update the repository the GitHub will show the modifications. Especially in the case of language changes (commas etc.) modifying the tex directly is the easiest way.

    This also means that from now on, the most recent version can be found from the GitHub, not from the Dropbox link used by this far. However, I will try to keep the Dropbox link somewhat up-to-date as well.

  5. I realized that indeed several publishers are not always consistent in applying their policies against preprints. So I agree with Samuli and Markus that it's worth "testing" their coherence. Also, it might be a way to trigger some discussion within the publishing organizations, which might ultimately change their policies, if open science becomes a popular way of doing science. In the end, they might not want to refuse good papers only because there's been a preprint (especially if competitors will publish those papers).


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