Wednesday, December 12, 2018

Current status of the project

22.11.2018 The first annual NMRlipids workshop is coming!

NMRlipids workshop 2019 May 15th to 17th

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 Quantifying the effect of bound charge on headgroup order parameters 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 (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 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:

10.10.2014 Together with Hubert Santuz we have started a GitHub organization It contains a repository: The idea is to collect all the relevant files related to the project there. There are already some files and there will be more. If you are familiar with git you can add your files by making a pull request. If you are not familiar you can also make as previously (add a link to a comment) and ask us to add it into the GitHub. Downloading the data should be straightforward without any understanding about the git system. It took a couple of hours for me to get familiar with the git system. The time was well spent and I recommend it to everyone.

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
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 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.

NMRlipids IV: Toward submission of the manuscript about PS lipids

I believe that the manuscript about PS lipids contains now all the essential content (see also the supplementary information). The main results are:
  • None of the tested models reproduces the PS headgroup order parameters within experimental accuracy but the best models suggest that the carboxyl group in serine headgroup does not rotate freely.  
  • Cation binding to bilayers containing PS lipids is overestimated in all the tested simulations, except in MacRog with potassium and CHARMM36 with the NBfix for the calcium. However, the latter underestimates the binding affinity.
  • The qualitative response of PS lipid headgroups to the bound calcium and dilution with PC lipids do not agree with experiments in any of the tested models, indicating that the force field development is necessary for MD simulation studies of PS lipids and their interactions with other biomolecules.
There is a todo list in the manuscript, mainly containing missing details. Current contributors, please check the list (also in the supplementary information). One question regarding many points in the todo list is that how much simulation details we should put in the supplementary information when the data is shared in Zenodo? When the details are well described in Zenodo (for example here), it may not be necessary to repeat all the information in the SI. However, cases where the data is not much described in Zenodo but the repository contains all the files having all the information about simulations (for example this) are more complicated. Are there any opinions about this? 

In addition, all kind of comments are welcomed, also from the people who have not contributed to the manuscript. At this point, I hope to have comments from as many people as possible, including also critical comments. 

If you have major concerns about scientific content, I hope to hear about that before the end of January 2019. If there are no major concerns, I hope that we could submit the manuscript by the end of February 2019. 

Wednesday, December 5, 2018

Correlation times of C–H bond direction in different force fields

We are starting a small project to see how well the correlation times of C–H bond vectors are reproduced in different force fields. We aim to simply follow the analysis of the R1 and τeff times as was done earlier by Tiago, Samuli, et al. for the Berger force field, but for all the different force fields available at the Zenodo repository of NMRlipids.

The plan is to not make this an official NMRlipids project, but still to do it fully openly; to this end, we warmly welcome anyone interested to follow the progress and to participate on GitHub!

Leftin and Brown have published experimental Rtimes for many different lipids in various temperatures and at various field strengths. Concerning the experimental τeff times, in Tiago's paper they are reported for POPC at full hydration and 298 K, and they have also been published for DMPC at low hydration and 300 K. However, as many of the trajectories at the Zenodo repository have DPPC, the experimental τeff times for DPPC at full hydration would be warmly welcomed.

Beyond force field comparison, possibly interesting physical questions to look from the data would be the effects of hydration, salts, and cholesterol on C-H bond dynamics. A possible extension could also be to look at the temperature dependence.

Hanne Antila and Markus Miettinen

Thursday, September 20, 2018

NMRlipids III: Quantitative measure for the force field quality needed

Progress in the NMRlipids III project about lipid-cholesterol interactions has been slow because the focus has been recently in improving ion binding to PC lipid bilayers and charged membranes.

After revisiting the manuscript with a serious intention to finalize the project, I think that we need to define a quantitative measure for the force field quality to simplify the discussion. For example, Berger model gives the best agreement with form factor data with high cholesterol content, but too large order parameters. On the other hand, Slipids give better order parameters with and without cholesterol but the form factor with high cholesterol concentrations is less good, and so on. This kind of discussion could be significantly simplified with a quantitative quality measure for the force field quality.

The quality measure could be also used to rank the force field quality in the databank collected from the contributions to the NMRlipids project and in further automatic force field development. The simplest measure to start with could, for example, sum up the deviation from the experimental order parameters for different segments and the deviation from experimental form factor using equation (3) from the SIMtoEXP publication. Similar measure has been recently introduced for proteins in solution.

Any kind of ideas and contributions about measuring the force field quality are welcomed.

Tuesday, September 18, 2018

NMRlipids IV: Challenges in evaluating counterion binding affinity to PS bilayers

Counterion binding to POPS lipid bilayers is signifincantly different between simulation models, as seen from density profiles along membrane normal in figure 1.
Figure 1:    Counterion densities of POPS lipid bilayer along the membrane normal from simulations with different force fields.

In the NMRlipids IV manuscript, we are trying to figure out which one these is the most realistic. In the NMRlipids II project we evaluated the sodium binding affinity to PC lipid bilayers using the changes of headgroup order parameters and electrometer concept. Similar experimental data is available for POPC:POPS (5:1) mixtures as a function of KCl, NaCl and LiCl concentration. This data is compared with different simulations in figure 2.
Figure 2:     Changes of the PC (left) and PS (right) headgroup order parameters as a function of added NaCl, KCl and LiCl from POPC:POPS (5:1) mixture at 298 K (except Berger simulations are (4:1) mixture at 310 K).
Rough conclusions could be that the binding of sodium and potassium is overestimated in Berger and CHARMM36 models, while Lipid17 performs better. Changes in MacRog model with potassium are somewhat overestimated but not systematically. However, these results are more difficult to interpret than the corresponding figure for PC lipids in the NMRlipids II, because zero point of the x-axis (added salt concentration) is not free of ions in this case. The systems always contain counterions when PS lipids are present and the binding affinity of these counterions differ between simulation models. Therefore, the changes of order parameters in figure 2 cannot be plotted against completely ion free state and the interpretation is more complicated.

The changes of PC headgroup order parameters with increasing amount of PS lipids give additional information about counterion binding affinity. According to the electrometer concept, the headgroup order parameters increase with increasing amount of negatively charged PS lipids, as seen in experiments and MacRog simulations with potassium in figure 3.
Figure 3:  Changes of PC (left panel) and PS (right panel) headgroup order parameters from POPC:POPS mixtures with increasing amount of POPS.
However, POPC headgroup order parameters are unaffected by POPS in CHARMM36 simulations with potassium and sodium counterions, and decrease in Berger simulations with sodium. This can be explained by overestimated counter ion binding in these simulations, which cancel the negative charge by the PS headgroups.

In conclusion, the results would suggest that sodium clearly overbinds in Berger simulations, both sodium and potassium slightly overbind in CHARMM36 simulations and most realisistic binding to PS containing bilayers is observed in MacRog simulations with potassium. The case of Lipid17 is little bit unclear because the relatively strong counterion binding in Figure 1 is not seen in Figure 2. The Lipid17 results are yet missing from Figure 3 because we do not have pure POPC simulation with Lipid14 at 298 K.

ToDo: My current suggestion is to do following. We conclude from this data that the MacRog simulations with potassium probably represent the most realistic counterion binding affinity to PS containing bilayers and compare its density profile to the results from other simulations in Figure 1. To finalize this part we still need the following data:
  1. Pure POPS MacRog simulation with potassium counterions at 298 K
  2. Pure POPC Lipid14 simulation at 298 K
  3. Ion density profiles from Lipid17 POPC:POPS (5:1) simulations with different ion concentrations for figure: (we already have the data in Zenodo in Amber format but we need to calculate the density profiles.)
Maybe we should also move current figures 7 and 8 to the supplementary information.

Fortunately, the calcium binding results seems to be more clear because changes in both simulations and experiments are larger.

Wednesday, July 4, 2018

NMRlipids IV: First draft of the manuscript about PS lipids

Thank you again for the 168 comments in the two previous blog posts about NMRlipids IV project (NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PE, PG and PS lipids and NMRlipids IV: Current status and reorganization of the manuscript) and numerous contributions to the GitHub repository.

First draft of the manuscript summarizing the results related to PS lipids is now compiled. As discussed previously, the goal is to first finish the manuscript about PS headgroup and then progress with PG and PE results separately. In addition to the up-to-date manuscript (pdf, tex) and supplementary information (pdf, tex), also the figures and data are available in the GitHub repository.

I believe that the manuscript already contains most of our conclusions, but several issues need to be addressed before we can start to prepare the submission. Most important current issues are listed here, accompanied with the names of persons who can hopefully help me to resolve the issues.
  1. We need slightly more detailed description of the NMR experiments by Tiago Ferreira. Also the results and discussion about the experiments, including Figure 1, needs to be polished.
  2. Atom names and dihedral notations should be made consistent between the chemical structures in figure 2, and dihedral angles distributions in  figures S6 and S7 by Pavel Buslaev. I am not sure if we could just the atom names currently used in figure 2, or if we need more labels. Slight polishing of figures S6 and S7 is also needed.
  3. The subjective ranking criteria in figure 4 by Markus Miettinen should be probably improved, see issue #4 in the GitHub repository.
  4. CHARMM36 data from POPC:POPS (5:1) mixtures with added NaCl would be highly useful for figure 6. CHARMM36 gives two maxima in the counterion density profiles in figure 5, while for example Lipid17 gives only one. From the right column of figure 6 we could see if this difference is reflected to the order parameter response of PS headgroup to the excess counterion concentration. Data from Gromos-CKP would also be useful for this. If someone has such data or is willing to generate it, let us know. 
  5. CHARMM36 simulations with the added CaCl2, but without the new NBfix, mentioned by Jesper Madsen would be useful for figure 9
  6. Lipid17 simulations ran with the Amber package, mentioned by Batuhan Kav, would be useful for figure 9
  7. Details of simulations by Thomas Piggot, Jesper Madsen, Fernando Favela, Batuhan Kav, Markus Miettinen, Josef Melcr and Matti Javanainen should be added in section S1 in the supplementary information (tex file here).
In addition, all comments regarding the current manuscript are welcomed. I will continue working with the manuscript and keep the the list updated.  

Thursday, April 12, 2018

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

One of the original goals of the NMRlipids project was to find a MD model that correctly describes cation binding to zwitterionic PC lipid bilayers. In the NMRlipids II project, we concluded that the currently available MD models typically overestimate cation binding and that none of them was accurate enough to capture calcium binding details to PC bilayers. Furthermore, the improved ion models available at the time were not sufficient to reproduce the correct binding behavior.

In early 2017, we started to develop a new MD simulation model of POPC in the group of Pavel Jungwirth. The goal was to improve one of the existing lipid force fields to reproduce the experimental Na+ and Ca2+ ion binding affinities to PC bilayers without destructing the ion-free bilayer properties. We assumed that cation binding could be improved by implicitly including the electronic polarizability to an existing lipid model by using the electronic continuum correction (ECC) [Leontyev et al. PCCP 13, 2613 (2011)]. ECC had been previously applied to ion parameters in Jungwirth's group by simply scaling the ion charges [Kohagen et al. J. Phys. Chem. B 118, 7902 (2014), Kohagen et al. J. Phys. Chem. B 120, 1454 (2016)]; we decided to extend this approach also to lipid models. Our original plan was to proceed using the open collaboration approach, that is, turn our initial development efforts into a NMRlipids project. Due to the surprisingly rapid progress, we, however, decided to finish the manuscript in the traditional way: It is now accepted to be published in the Journal of Physical Chemistry B [J. Melcr, H. Martinez-Seara, R. Nencini, J. Kolafa, P. Jungwirth, and O.H.S. Ollila J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.7b12510]. All our data and files are available in the GitHub repository and in Zenodo (see e.g. DOI: 10.5281/zenodo.1118265), similarly to the NMRlipids projects.

Shortly, we used the Lipid14 parameters of POPC as a starting point and applied ECC to the headgroup and glycerol backbone atoms. The scaling factors of 0.8 and 0.89 were used for partial charges and LJ radii, respectively. Numerical values of the scaling factors were tuned to reproduce the experimentally observed calcium binding affinities as well as structural details without additional ions. Figure 1 shows comparison between the developed ECC-POPC model, Lipid14, and experiments. For more details, further analysis, data, and parameter files see the manuscript in press, the GitHub repository, and Zenodo.

Figure 1: Response of the headgroup order parameters (which is a direct measure for ion binding affinity, see NMRlipids IIto added CaClin the ECC-POPC model, in the Lipid 14 model, and in experiments.

We are currently running further tests for the developed ECC-POPC model and extending the development to negatively charged phosphatidylserine (PS) lipids. The development of ECC-PS lipids will be done in parallel with the NMRlipids IV project. The GitHub repository for the ECC-PS model development will be publicly available, but at least for now it is separated from the NMRlipids project core.