Towards first submission to journal

The new version of the first manuscript is now updated to arXiv: http://arxiv.org/abs/1309.2131v2. 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:
https://www.dropbox.com/s/guf88xwi25u72ap/HGmodel_draft3.pdf?dl=0

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.