Friday, February 6, 2015

The first draft of the ion-lipid interaction manuscript

[update 14.12.2015] Different force field was used for CHARMM36 ions than I tought.

[update 16.4.2015] I have created an own GitHub Repository for this project. The links are updated.

I have now written the first draft of the manuscript considering the ion-lipid interactions discussed in this blog. All the manuscript files (written with LaTex) are in GitHub. The pdf version the manuscript with ToDo list is also available through link, in addition to GitHub.

I think that there are few simulations more which we definitely have to run for this manuscript:
  • Orange model with higher concentration of NaCl (I will do this).
  • CHARMM36 model with CaCl\(_2\) (the data contribution from someone already having this data would be excellent. I if this does not happen, I will do it).
In addition, it would be very interesting to get some results with different NaCl and CaCl\(_2\) concentrations from the modified CHARMM36 ions by Venable et al. According to the paper, the parameters improve the ion binding to the charged lipid bilayers. I think that the data with these parameters would be highly relevant, however I do not have time to do it now.  The force field by Venable et al. is already used in the current CHARMM36 simulations with NaCl, see comment on 14.12.2015.

All kinds of comments about the manuscript are welcomed from everybody (also from people who are not contributors yet). You can submit your comments by commenting this post, or you can directly fork the GitHub repository and make a pull request.

The authorship of the manuscript will be offered for everyone who has commented the blog, according to the "on the credits post". The final decision on authorship will be made by invited individuals themselves based on their self-assessment of their scientific contribution to the project. The separate authorship query is sent to to all contributors with email and authorlist will be updated according to the replies.