## Friday, October 22, 2021

### Current status of the project

22.12.2021 The slides about the current status of the NMRlipids databank presented in the online meeting on 17.12.2021 are available from here.

9.12.2021 Online meeting on the development of NMRlipids databank and project will take place on 17.12.2021. Program and more details available from here. For Zoom invitation, send email to samuli.ollila (@) helsinki.fi

8.12.2021 Due to the current COVID-19 regulations of the venue, we had to postpone the NMRlipids winterschool 2021 to the first half of the next year. Nevertheless, there will be a developers meeting online in December. More information will follow when we have the new dates available.

22.10.2021 NMRlipids winterschool 2021 will be organized on 15.-17.12.2021 in Helsinki with the option for online participation. Aim of the school is to give introduction for the automatic and flexible analyses over hundreds of lipid bilayer simulations using the NMRlipids databank. Registration and further information from this link.

24.9.2021 NMRlipids20 workshop outcomes post was published

18.8.2021 NMRlipids IVb manuscript with the updated title, Inverse Conformational Selection in Lipid–Protein Binding, is now published in the Journal of American Chemical Society.

24.3.2021post was published

19.2.2021 Online meeting on the NMRlipids datanbank and the NMRlipids VI project on polarizable force fields will take place on 26.2.2021 in Zoom. If you are interested to join, but have not received email invitation, please send me email. The schedule of the meeting is available in here.

23.12.2020 NMRlipids VI: First results from polarizable Charmm-Drude force field post written by Batuhan Kav was published.

3.7.2020 Online meeting about the NMRlipids databank post summarizing the outcomes of the meeting was published.

22.6.2020 We are having a NMRlipids online meeting about the development of the NMRlipids databank at 16.00 CET on Monday 29th of June. After a short presentation by Samuli Ollila on the current status, we will discuss on urgent topics related to the databank development. This discussion was originally planned to take place in the postponed NMRlipids20 meeting. The meeting is open for everyone. I will share a link by email to NMRlipids contributors before the meeting. If you are not a contributor yet, but want to join to the meeting, please send me email.

7.4.2020 NMRlipids VI: Polarizable force fields post and beta version of the new data contribution script were published.

1.4.2020 Due to the COVID-19 pandemic situation, the NMRlipids20 workshop is postponed. The workshop will be organized as soon as possible after the pandemic is over.

5.2.2020 The NMRlipids20 workshop takes place on 13-15th of May in Prague, Czech Republic. Drop us an email if you are interested to join.

2.10.2019 the NMRlipids IV manuscript about PS lipids is now accepted to be published in the Journal of Physical Chemistry B

12.9.2019 Revised version of the NMRlipids IV manuscript about PS lipids is now submitted to the Journal of Physical Chemistry B

26.6.2019 The NMRlipids IV manuscript about PS lipids is now submitted to the Journal of Physical Chemistry B

31.5.2019 The first annual NMRlipids workshop post was published

23.4.2019 NMRlipids IVb: Assembling the PE & PG results post was published

22.11.2018 The first annual NMRlipids workshop is coming!

20.9.2018 Homepages of my group are now published. Check and share also the announcement of open Ph.D. student position.

20.9.2018 NMRlipids III: Quantitative measure for the force field quality needed post was published

18.9.2018 NMRlipids IV: Challenges in evaluating counterion binding affinity to PS bilayers post was published

15.9.2018 Google has launched a new Dataset search engine. It seems to find the data from NMRlipids project very well.

13.9.2018 Poster presented about NMRlipids IV project in Tiny Lip­ids With Grand Func­tions workshop in Helsinki, Fin­land, 19 - 22 Au­gust 2018:

4.7.2018 A lot of data has been contributed to the NMRlipids III and IV projects. Especially the NMRlipids III project is delayed because the main focus has recently been in the ion-membrane interactions. Currently the first priority is to finish the manuscript about PS lipids from NMRlipids IV, the second to finish the manuscript about lipid-cholesterol interaction from NMRlipids III, and the third to progress the manuscript about PE and PG lipids.

4.7.2018 NMRlipids IV: First draft of the manuscript about PS lipids post was published.

3.5.2018 Samuli Ollila received a academy research fellow position from the academy of Finland for five years. The research plan includes the development of the NMRlipids project.

13.4.2018 PS-headgroup order parameter comparison now also shows results for Amber Lipid 17:

12.4.2018 New NMRlipids-related publication: Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization post was published

30.1.2018 Database of the NMRlipids simulations and experiments post was published.

22.12.2017 NMRlipids IV: Current status and reorganization of the manuscript post was published

8.12.2017 Results from CHARMM36 simulation with cationic surfactants was added to Quantifying the effect of bound charge on headgroup order parameters post.

27.7.2017 post was published.

31.3.2017 NMRlipids III: Preliminary version of the manuscript post is published.

9.3.2017 NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PE, PG and PS lipids post is published. Almost any kind of simulations of these lipids in bilayers would be useful at this stage.

15.2.2017 My activity in NMRlipids project has been low during the last months due to other commitments. However, I have now again possibility to advance NMRlipids III and IV projects (updates will follow soon). We have also published a blog post about the future of NMRlipids project.

29.11.2016 NMRlipids project will be presented in PHOS16 Conference (Philosophy and History of Open Science) held in Helsinki on 31.11.-1.12.2016. There should be also live stream available.

12.11.2016 NMRlipids II manuscript Molecular electrometer and binding of cations to phospholipid bilayers accepted for publication in Physical Chemistry Chemical Physics, and the preprint is available on the journal web page.

16.10.2016 Zenodo has been updated as described in their news page. There are a lot of improvements but this one is probably the most important for us: "The current 2GB per file limit is removed, in favour of a 50GB per dataset limit". This means that we do not have to split the trajectories in 2GB pieces anymore.

7.10.2016 The final version of NMRlipids II manuscript (lipid-ion interactions) submitted to Physical Chemistry Chemical Physics.

9.9.2016 NMRlipids II manuscript (lipid-ion interactions) "accepted for publication after revisions" to Physical Chemistry Chemical Physics.

13.7.2016 NMRlipids II manuscript (lipid-ion interactions) has been now submitted to Physical Chemistry Chemical Physics.

1.7.2016 NMRlipids III: Preliminary observations post was published.

30.5.2016 Toward submission of NMRlipids II publication (lipid-ion interactions) (2) post was published.

20.5.2016 The new data delivered for NMRlipids II project raised a question about the order parameter responses on bound charges in CHARMM36 model. If you have CHARMM36 simulation data of PC bilayer with known amount of charged amphiphiles and you are willing to share it for the project, please let us know.

24.2.2016  Our goal from the beginning has been to immediately publish all the scientific content related to the project. One relevant part of the content are discussions between reviewers and authors during the peer review process. We have now published two peer reviewed articles: NMRlipids I and NMRlipids V. In both cases we have asked from the editor if we can publish also the reviewers' comments since everything else is public. As expected, in the NMRlipids I case the Journal of Physical Chemistry staff replied that this is not possible. However, editorial and publishing teams of BBA Membranes'  were positive about publishing the referees' comments in the case of NMRlipids V publication. Both referees were also sympathetic to the idea. However, one of them declined stating permission to make comments available should be asked a priori, at the same time referees are invited to review a paper. This is an important learning point from this experience.

25.1.2016 The review written in the NMRlipids V project has been now accepted to be published in BBA - Biomembranes and is available also from their webpage.

19.1.2016  Does the glycerol backbone structure depend on initial structure? post was published.

21.12.2015 Towards submission of NMRlipids II publication (lipid-ion interactions) post was published.

24.11.2015 The review written in the NMRlipids V project has been now submitted.

29.10.2015 The NMRlipids I publication is already available also through the journal website.

28.10.2015 The first manuscript (NMRlipids I) based on the data and discussions presented through this blog is now accepted to be published in the Journal of Physical Chemistry B. We thank all the contributors and followers for courage to participate this project.

13.10.2015 We have received a new revision request for the first manuscript (NMRLipids I project). The first version of the reply is already in GitHub. There were essentially no new comments compared to the first revision round so I will not make a new post for this. If you have comments, you can comment the Revision requested for the first manuscript post or GitHub. If there will not be objections I will submit the revision on Friday this week (16.10.2015).

28.9.2015 NMRLipids V project: Review about validations of membrane MD simulations was published. This is a project to write an invited review on a topic strongly related to the blog content.

28.9.2015 The title of the blog has been changed to "The NMRlipids project: Open Collaboration to understand lipid systems in atomistic resolution".

24.9.2015 The NMRLipids project will be discussed in Mindtreck 2015 conference in Tampere. At least one of the sessions may be live streamed, see the facebook event.

22.8.2015 The revised version of the first manuscript is now submitted.

20.7.2015 Revision requested for the first manuscript post was published.

6.7.2015 About page describing the different subprojects and Workflow page suggesting new workflow for these projects are now published.

26.5.2015 The first manuscript produced in this blog was considered to be
"primarily directed toward an audience of specialists doing closely related work and that lack a clear description of impact on the broader field of chemistry" by the editor of the Journal of American Chemical Society and it was rejected without peer review process. Thus, the manuscript has been now submitted to the Journal of Physical Chemistry (another journal ran by american chemical society).

15.5.2015 The first manuscript produced in this blog is now submitted to the Journal of American Chemical Society.

12.5.2015 The first manuscript produced in this blog will be submitted to the Journal of American Chemical Society by the end of this weeḱ.

25.3.2015 Mapping scheme for lipid atom names for universal analysis scripts post was published.

17.3.2015  Towards first submission to journal (2) post was published.

9.3.2015 Current and future activity post was published.

6.3.2015 Samuli will talk about this project in the event organized by the Open Knowledge Finland (OKFFI) on 10.3.2015 in University of Helsinki. There will also live stream from the event through this link http://vn-rec.it.helsinki.fi (user: video, pw: video)

6.2.2015  The first draft of the ion-lipid interaction manuscript was published.

16.1.2015 Towards first submission to journal post was published.

16.1.2015 The current version of the new manuscript is now updated to arXiv http://arxiv.org/abs/1309.2131v2. There will be soon a new post about the further proceeding.

23.12.2014  New version of the manuscript (2)  post was published.

21.11.2014 New manuscript written on the results reported in this blog is available for commenting: New version of the manuscript. The manuscript covers only the results for fully hydrated bilayers, effect of dehydration and effect of cholesterol. A separate manuscript will be written about ion-lipid interactions.

18.11.2014 New manuscript written about the results reported in this blog will be made available for commenting on Friday 21th of November.

12.11.2014 The post About glycerol conformations is now updated. The incorrect stereospecifity in GAFFlipid for g$$_1$$ segment was due to the intial structure downloaded from lipidbook, not due to the GAFFlipid force field. The updated figure with the results:

7.10.2014 We have added a new page called Data Contributions as an attempt to arrange the discussion. The idea is that all the new data would be sent by commenting the Data Contibutions page. Yet, let us keep the other comments under each separate post.

1.9.2014  The post About glycerol conformations was published.

20.8.2014 Presentations describing the nmrlipids project in the International Workshop on Biomembranes - From Fundamentals to Applications were posted.

19.5.2014 The post Towards a new version of the manuscript was published.

13.5.2014 To Do List has been added as a page in the top panel.

2.5.2014  The post Response of headgroup and glycerol order parameters to changing conditions: Results, reviewing the current results for the responses of the headgroup and glycerol order parameters to the changing conditions, was published.

29.4.2014 The R/S hydrogen labeling was wrong for MacRog in the previous plot. The correct one was reported by Matti Javanainen. Here is the new plot:
Now also the MacRog is in good agreement with experiments, in addition to CHARMM.

24.4.2014 Based on discussions with Antti Lamberg and Patrick Fuchs we have now plotted the results with the sign, and the R/S hydrogen labeling

It seems that the CHARMM36 results are in the best agreement with experiments. (However, the R/S hydrogen labeling in MacRog has to be still confirmed).

16.4.2014 Patrick wrote a comment on how to tell R and S and hydrogens apart.

11.4.2014 The lipid forcefield comparison at full hydration updated—now contains results for 12 force fields.

10.4.2014 The post On the signs of the order parameters was published.

10.4.2014 We have added a page containing information about the authors of the project (see the top panel).

31.3.2014 The new version of order parameter calculation script is now available at https://www.dropbox.com/sh/au7cglb7i4o0uvy/65dRNta_bM
It will now calculate also the sign. Also the *hdb file to protonate the Berger lipids with Gromacs g_protonate tool is now available. Note that there was a bug in the script shared in the original figshare package: It takes only the first 75 lipids in to account. Thus, if you have used it for the larger systems you have not taken all the available statistics into account. For my own Berger results, this makes a very small difference though. It would be very useful if someone would make a tool which would directly calculate the order parameters from the Gromacs *trr file.

14.3.2014 The lipid force field comparison at full hydration was published.

9.3.2014 Antti demonstrated that it is possible to get a very good agreement with the experimentally measured order parameters by simply sampling a large set of randomly modified dihedral potentials, choosing the most promising ones, and repeating this randomised refinement a few times.

25.2.2014 This is our new front page: A simple list the most relevant events, ordered by date. Its purpose is to help you keep up with what is happening on the blog—in posts as well as in comments.

25.2.2014 Blog post discussing the accuracy of order parameter measurements was published.

16.2.2014  Samuli gave a presentation related to the nmrlipids-project at the Biophysical Society meeting.

13.2.2014 The first attempt to modify the Berger dihedral parameters was reported with a preliminary conclusion that removing all dihedral potentials improved the choline- but impaired the g1 order parameters.

12.2.2014  Our current knowledge of the behaviour as a function of dehydration gathered into a single plot.

23.1.2014  Our current knowledge of the behaviour as a function of ion concentration gathered into a single plot.

23.1.2014  Our current knowledge of the behaviour as a function of cholesterol content gathered into a single plot.

21.1.2014 Our current knowledge of the full hydration behaviour gathered into a single plot.

10.12.2013 Patrick filed a Redmine Bug about reaction field simulations with Gromacs 4.0.7 not being reproducible with 4.5.3., which he commented first here on Oct 25th.

29.10.2013 Samuli wrote a guest post to the MARTINI group blog: PN vector orientation not a good measure for evaluating phospholipid force field performance, use head group order parameters instead.

2.10.2013 The first results were shortly reviewed and some short term goals were set in a new blog post.

13.9.2013 The first comment and the first contribution.

10.9.2013 A post discussing the motivation for the project:
and the first three scientific posts were published:

9.9.2013 The first version of the manuscript was published.

11.7.2013 The policy for publication credits was published.

3.7.2013 The nmrlipid.blogspot.fi was opened with a post that stated our aim.

28.6.2013 The project was first time publicly discussed in a presentation at the Biological membranes: challenges in simulations and experiments -meeting in Paris.

## Friday, September 24, 2021

### NMRlipids20 workshop outcomes

Thirteen contributors participated to the second NMRlipids workshop organized on 6th-9th of September in Prague, Czech Republic.

Three talks on topics related to the NMRlipids project were given on the first day: Pavel Jungwirth presented results on how charge scaling can improve MD simulation quality without additional computational cost, Hanne Antila presented results from a automatic force field optimization algorithm, and Ricky Nencini presented evaluation of drug molecule binding affinities in MD simulations against NMR data.

Batuhan Kav presented the current status of the NMRlipids VI project on polarizable force fields. The main conclusion from the talk and consequent discussion was that the headgroup conformational ensemble and ion binding in Drude model is significantly worse than in original CHARMM36, most likely because forking and signs of headgroup order parameters are not taken into account during parameter optimization. The results from AMOEBA simulations are not yet available due to practical issues, but consensus was that those would be highly relevant.

Second day was opened by Samuli Ollila with the presentation on the current status of the NMRlipids databank. This was followed by work in three groups:

1. Quality Evaluation. Goal: Define the quality measures for order parameters, find robust code for form factor calculation and include this into the quality measure. Outcomes: Quality measure for order parameters, S=-log(P), where P is the probability mass within the experimental error for a normal distribution around simulation result (mean = order parameter from simulation, standard deviation = error of order parameter from simulation). Implementation of this was preliminary tested and committed to the QualityEvaluation.py. A new form factor code with python is now implemented, preliminary tested, and committed into the MATCH repository
2. Extension of the databank to other than Gromacs programs. Goal: Define the required files needed to add simulations ran with other than Gromacs program into the databank. Outcomes: Possibility to incorporate OpenMM data was implemented. The required files are the trajectory (e.g., in dcd format), structure (e.g., in pdb format) and either xml file or inp file. Force field / topology information can be optionally given as psf file. This is implemented in branch of Anne Kiirikki, but not yet merged to main branch.
3. Analysis of the data. Goal: Test and improve the codes for the analysis of the databank. Outcomes: A new class that makes the analysis of databank significantly easier was introduced. An example code was implemented and commited. Also a new way to organize the information about molecular composition in the databank README.yaml files was proposed to ease the writing of analysis codes. The implementation of this is currently in progress by Anne Kiirikki.

In addition to these, several other topics were touched during discussions. These include, for example, practical ways to handle united atom simulations, stereo specific information in mapping files, sanity checks for the data, NMRlipids III project, and other potential data repositories than Zenodo. However, practical steps to progress these topics were not taken.

In conclusion, the workshop was again highly useful, at least for the NMRlipids project, and hopefully also for the participants. Thank you for all the participants!

## Wednesday, March 24, 2021

### NMRlipids IVb: Toward submission of the manuscript with PE and PG results (2)

The manuscript is now substantially updated based on comments to the previous post and discussions in the online meeting held on 12th of January 2021. All force field evaluations are moved to the supplementary information, analysis of lipid structures from PDB is improved, illustration of similar structures of different lipids bound to different proteins is added to figure 4, and dihedral distributions in figures 2 and 3 are changed to relative energies in kT units.

I believe that the manuscript is close to the submission stage, and I would like to submit it within one month from now, i.e., before 24th of April 2021. Therefore, the last opportunities to comment the manuscript are approaching.

Before the submission, the figures 1 and S1-S3, and experimental and simulation details needs to be polished.

We also need a good title for the article. The title is discussed in this issue.

In addition to these issues, I would be happy to have any comments on the manuscript as soon as possible, particularly if you have major comments on the content of the manuscript.

## Wednesday, March 3, 2021

### Second online meeting on the NMRlipids databank

Second online meeting on the NMRlipids Databank was held on 26th of February 2021. The slides presented in the beginning of the meeting are here. The main questions discussed in the meeting were related to the information that should be indexed in the databank, and the properties that should be automatically analyzed from simulations.

Although the beta version of the databank still exists in the NMRlipids IV project repository, a specific repository for the NMRlipids Databank is now available. Further development of the databank will be done this repository, while the beta version will be used for applications related to the NMRlipids IV project.

A publication introducing the databank with some highlight applications will be prepared (discussion opened in this issue). Original NMRlipids authorship rules will be applied in the first publication of the databank with two exceptions: Samuli Ollila will be the last author and Anne Kiirikki will be the first. The authorship rules for the future publications regarding the updates in the databank are yet to be carefully discussed and decided on.

Outcomes of the discussion on 26th of February 2021 were:

1. It was decided to include the following optional inputs by the contributors (in addition to the current indexing information listed in the slides): PUBLICATION INFORMATION, SOFTWARE VERSION, AUTHOR INFORMATION AND CONTACT, CPT FILE, LOG FILE, and TOP FILE. In addition to these, the date of running the AddData.py script will be automatically saved to the index files. DONE
2. The input file format for AddData.py will be changed to yaml. DONE
3. Inclusion of the information on lipid isomers into the databank was discussed, but practical solutions are not yet clear. Further discussions will be in this issue.
4. Automatic methods to determine (based e.g. on area per lipid and PCA analysis) how equilibrated the contributed trajectories are, will be investigated. Further discussion will be in this issue.
5. Consistency of the indexed data will be checked by comparing the total number of atoms between the databank and the actual simulation. Also some other potential sanity checks were discussed. Further discussion will be in this issue.
6. Properly functioning code for the form factors is needed in the near future. Further discussion will be in this issue
7. Databank will be made functional also with at least OpenMM and Amber data before the first publication. Further discussion will be in this issue.
In addition, Anne Kiirikki is working with the databank containing experimental data in the form that it could be automatically linked with the MD simulation databank.

As the next step, we plan to work out the points 1 and 2 from the above list. Then we will probably add all the currently available data into the databank, and continue to work on points 3-7.