tag:blogger.com,1999:blog-1283194685237019772.post2558233326704758195..comments2024-03-26T17:11:28.045+02:00Comments on The NMRlipids Project: New version of the manuscript (2)markus.http://www.blogger.com/profile/05973383391755193687noreply@blogger.comBlogger43125tag:blogger.com,1999:blog-1283194685237019772.post-89857271768212148002015-02-10T11:56:06.571+02:002015-02-10T11:56:06.571+02:00All your remarks are interested and could improve ...All your remarks are interested and could improve the graph but unfortunately I'm not sure I can satisfy them. <br /><br />Since I'm using the plot.ly library (same as gnuplot, matplotlib,mpld3,..), everything is done automatically (interactivity, plot, zoom, etc). From the documentation, your remarks are not possible right now. Just the zooming is possible : You have a series of button in the top right of the graph to play with zooming.<br />In the bottom left, you also have a the embed code (in html) to insert the graph in a webpage.<br />Anonymoushttps://www.blogger.com/profile/12407540570391825798noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-19835104723387780182015-01-31T01:04:06.902+02:002015-01-31T01:04:06.902+02:00Great, very nice! Quick thoughts that came to my m...Great, very nice! Quick thoughts that came to my mind:<br /><br />1) Would it be possible to allow for zooming into (or out of) the data? Automatic zooming when new data requires it would also be cool.<br /><br />2) Maybe the initial figure could be just with the experimental values and sweet spots? Then the viewer could click the simulation data on. (In this case there would need to be a button for turning on all the the data on at once, so one would not need to click each one separately if one wants to see all data.)<br /><br />3) A cool function (if such exist ready-made) would be if the plot would reorder the dots to maximize visibility depending on what is being shown.<br /><br />But these are just quick thoughts. Great work!markus.https://www.blogger.com/profile/05973383391755193687noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-11488486611888575692015-01-30T13:46:16.733+02:002015-01-30T13:46:16.733+02:00I compiled all the data and I made a plot almost i...I compiled all the data and I made a plot almost indentical that yours.<br />Here the link : https://plot.ly/~HubertSantuz/72/lipid-force-field-comparison/<br /><br />I'm still have to highlight the "sweet spots", change the marker type when errors bars are present and rearrange a little bit the legend but the proof of concept is here!<br /><br />Let me know what you think.Anonymoushttps://www.blogger.com/profile/12407540570391825798noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-61937817724431459622015-01-28T14:57:32.168+02:002015-01-28T14:57:32.168+02:00I uploaded on Zenodo all the files dealing with si...I uploaded on Zenodo all the files dealing with simulations using Poger's lipids (GROMOS 53A6_L). Here are the doi:<br /><br />With reaction field electrostatics<br />1) Traj RF: http://dx.doi.org/10.5281/zenodo.14592<br />2) Traj RF2: http://dx.doi.org/10.5281/zenodo.14591<br /> --> This is the traj I tested with different GROMACS versions. The pdf showing the results is located on the same Zenodo record (direct link to it: https://zenodo.org/record/14591/files/Comments_area_different_gmx_versions.pdf).<br /><br />With PME electrostatics<br />3) Traj PME: http://dx.doi.org/10.5281/zenodo.14594<br />4) Traj PME2: http://dx.doi.org/10.5281/zenodo.14595<br /> --> this is the two traj that were used in Fig 2<br /><br />Apart from that, Fig 2 is really nice with signs included. One tiny typo I noticed in the current version of the manuscript (about my affiliation p1): it's currently written "Institut Jacques Monod, CNRS, Universit Paris Diderot, Sorbonne Paris Cit, Paris, France" because the french accents do not show up. If it's not possible to write "Université" and "Cité" with the french acute accent, we may write "Institut Jacques Monod, CNRS, Universite' Paris Diderot, Sorbonne Paris Cite', Paris, France".<br /><br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-8997431903618955062015-01-26T11:07:06.612+02:002015-01-26T11:07:06.612+02:00Hi,
My simulations files are now on Zenodo :
POPC...Hi,<br /><br />My simulations files are now on Zenodo :<br />POPC Charmm36: http://dx.doi.org/10.5281/zenodo.14066<br />POPC 20% Chol Charmm36: http://dx.doi.org/10.5281/zenodo.14067<br />POPC 50% Chol Charmm36: http://dx.doi.org/10.5281/zenodo.14068<br /><br /><br />Anonymoushttps://www.blogger.com/profile/12407540570391825798noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-74960341893854853922015-01-22T14:00:00.091+02:002015-01-22T14:00:00.091+02:00All the up-to-date data is now in GitHub:
https:/...All the up-to-date data is now in GitHub:<br /><br />https://github.com/NMRLipids/nmrlipids.blogspot.fi/tree/master/DATAreportediINblog<br /><br />Maybe someone wants to test making an interactive plot of it? In the repository there is also the gnuplot script I am using to create our current static pdf.markus.https://www.blogger.com/profile/05973383391755193687noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-21720246590473737102015-01-17T15:02:43.559+02:002015-01-17T15:02:43.559+02:00As the reproducibility-issue [1] with GAFF (too sm...As the reproducibility-issue [1] with GAFF (too small areas-per-lipid compared to those reported by Dickson et al.) was never solved, we probably should discuss it in the Methods.<br /><br />[1] http://nmrlipids.blogspot.com/2013/10/welcome-if-you-are-new-here-reading.html?showComment=1381932164332#c7642197130088592128markus.https://www.blogger.com/profile/05973383391755193687noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-30196160310173345692015-01-15T12:33:37.936+02:002015-01-15T12:33:37.936+02:00Hi,
To continue with the interactive plot, there ...Hi,<br /><br />To continue with the interactive plot, there exist the tool called "plot.ly" which allow to make interactive graphs whith python,R, whatever and upload them into your account on their website. It's then really easy to share and collaborate on a graph and remove the need to host the interactive graph.<br /><br />I played with your data in here the result : https://plot.ly/~HubertSantuz/38<br />And here the script used : https://gist.github.com/HubLot/8af8045a6e002b0a893e#file-interactive-plot-with-plotly-pyAnonymoushttps://www.blogger.com/profile/12407540570391825798noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-67080433068369064112015-01-14T17:17:32.757+02:002015-01-14T17:17:32.757+02:00Sorry, Markus is right. t=30 ns for equilibration ...Sorry, Markus is right. t=30 ns for equilibration and 20 ns for calculations. t_sim(ns) = 50 and t_anal(ns) = 20.Anonymoushttps://www.blogger.com/profile/00656662181573495590noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-77940335120991476882015-01-14T13:55:31.213+02:002015-01-14T13:55:31.213+02:00About putting to Zenodo: Do you mean the files use...About putting to Zenodo: Do you mean the files used for Amber to Gromacs conversion? This may be reasonable, if they can be used to reproduce the conversion used in the publication. Then we could cite them. As far as understand, the original Amber files were taken from the Lipidbook so they are already available, which should be enough? <br /><br />Little bit annoying thing in Zenodo is that one cannot modify or add the files in the datasets after submission. For this reason, it might be better to keep all the stuff which is somehow in progress in GitHub, and add to Zenodo only when citation is needed.<br /><br />I have now added you as an author for the GAFFlipid and Lipid14 data sets in Zenodo, since you have done the force field files.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-16491568038977094532015-01-14T13:41:43.970+02:002015-01-14T13:41:43.970+02:00This may be an overkill. I have changed the "...This may be an overkill. I have changed the "tilting" to "reorienting" for now, however we can still think about this.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-12223328644419729282015-01-14T13:31:41.736+02:002015-01-14T13:31:41.736+02:00So in this case it should read "The system wa...So in this case it should read "The system was simulated for 30 ns in the NP$\gamma$T ensemble (Nose-Hoover style thermostat and barostat with anisotropic pressure coupling) at 323 K and 1 bar with timestep of 1 fs, the last 20 ns of the simulation was used for calculation of configurational averages."<br /><br />Right?Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-27216213486869074252015-01-14T12:51:11.393+02:002015-01-14T12:51:11.393+02:00Hi Marius,
This looks totally awesome!
I especia...Hi Marius,<br /><br />This looks totally awesome!<br /><br />I especially like the ability to zoom in for greater detail. Also since the code is in python it is straightforward to load new order parameter data into the array as more data is created. Big thanks for this, the python version is definitely the way to go. I like it very much.<br /><br />-JukkaJukka Määttähttps://www.blogger.com/profile/10063290967123430994noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-8179887685251098712015-01-14T12:35:27.678+02:002015-01-14T12:35:27.678+02:00No, t_sim(ns) = 30 and t_anal(ns) = 20.No, t_sim(ns) = 30 and t_anal(ns) = 20.Anonymoushttps://www.blogger.com/profile/00656662181573495590noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-63309944710027707442015-01-14T11:22:07.424+02:002015-01-14T11:22:07.424+02:00I played a little with the mpld3 library and the r...I played a little with the mpld3 library and the result looks promising http://bit.ly/1u3zF6z. The Python code used to generate the standalone html file is here https://gist.github.com/mretegan/36d8fc6a35daf1528229#file-interactive_plot-pyMariushttps://www.blogger.com/profile/09230639898850694481noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-20243941988664402902015-01-14T09:56:26.703+02:002015-01-14T09:56:26.703+02:00I very much like the idea of having an interactive...I very much like the idea of having an interactive infographic online to support the printed figure. A bonus would be that we could keep it up to date as more data is created. Unfortunately I (at least so far) lack the skills to do such a figure.markus.https://www.blogger.com/profile/05973383391755193687noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-9655614361151760982015-01-13T15:53:52.215+02:002015-01-13T15:53:52.215+02:00Hi,
I've got a somewhat crazy optional idea f...Hi,<br /><br />I've got a somewhat crazy optional idea for Fig. 2. <br /><br />This won't address the issues of the print version although I think it's really, really clear considering how much data is in the figure. <br /><br />So, I thought what if we also make a dynamic online-version of Fig. 2 where one could pick the force fields one wants for easier comparison? I fiddled with some data and did a proof-of-concept (contains old Github data for Gaff/lipid14 only): https://infogr.am/order-parameters<br /><br />I don't have expertise to do this properly but ideally one could make a similar plot of all the data (using perhaps CSS/html5/javascript instead of ready-made websites) and upload it to the web or in the blog.<br /><br />Now, the idea is to provide a link to it in the manuscript IN ADDITION to the print figure. The link could e.g. be put to the figure caption. Now I'm hoping someone here knows the web-standards well enough to make such a figure.<br /><br />-JukkaJukka Määttähttps://www.blogger.com/profile/10063290967123430994noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-14651052888404764202015-01-13T12:18:36.896+02:002015-01-13T12:18:36.896+02:00Here are my comments for points 59 and 60. Should ...Here are my comments for points 59 and 60. Should I put these files on Zendo. Should I put the original AMBER files on Zendo? The Gromacs compatible files are already included with the simulations that Samuli performed using the two FF.<br /><br />59) The force field parameters were generated using files obtained from the Lipidbook website (http://lipidbook.bioch.ox.ac.uk/package/show/id/150.html). The conversion to Gromacs compatible formats was performed using the acpype tool (10.1186/1756-0500-5-367). The accuracy of the conversion was check by calculating the total energy of a single POPC lipid molecule using the sander program which is part of the AmberTools14 (10.1002/wcms.1121) package and Gromacs 4.6.5. A difference of 0.002 kcal/mol was obtained between the two programs.<br /><br />60) The Amber compatible force field parameters were generated using the tleap program which is integrated in the AmberTools14 package (10.1002/wcms.1121). A workflow similar to the one used previously for the conversion and validation of the GAFFLipid parameters was followed here. As before, a negligible energy difference of 0.003 kcal/mol was obtained between the two programs.Mariushttps://www.blogger.com/profile/09230639898850694481noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-62855508714581595812015-01-12T17:01:16.579+02:002015-01-12T17:01:16.579+02:00Thanks KnQMe_4NuspqF2dqnJfBC86JFgANZmaEqZg-,
I ha...Thanks KnQMe_4NuspqF2dqnJfBC86JFgANZmaEqZg-,<br /><br />I have now included these changes into the manuscript.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-2240212719691405352015-01-12T12:36:54.727+02:002015-01-12T12:36:54.727+02:00To make it evident to the reader that we are not u...To make it evident to the reader that we are not using a straw man argument when discussing the umbrella model, a direct quote from the original paper would maybe be in order here? That is, we would write something along the lines:<br /><br />For example, the Umbrella model suggests that "phospholipid head- groups provide 'cover' to shield the nonpolar part of cholesterol from exposure to water" such that "as the cholesterol content in a bilayer increases, polar phospholipid headgroups reorient in order to provide more coverage per headgroup for the increasing fraction of cholesterol molecules" [cite Huang 1999]. In the Superlattice model cholesterol acts as a spacer for the headgroups thus increasing their entropy and dynamics…<br /><br />Should we decide to do this, we probably should use a direct quote also to describe the Superlattice model.markus.https://www.blogger.com/profile/05973383391755193687noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-16677451012958087612015-01-12T11:34:18.734+02:002015-01-12T11:34:18.734+02:00This is direct quotation from the Umbrella model p...This is direct quotation from the Umbrella model paper [Biophys. J. 76, 2142–2157 (1999)]:<br />"When cholesterols are incorporated into a phospholipid bilayer, phospholipid headgroups provide “cover” to shield the nonpolar part of cholesterol from exposure to water. This is illustrated schematically in Fig. 10 a. Phospholipid headgroups act like umbrellas. The space under the headgroups is shared by acyl chains and cholesterols. As the cholesterol content in a bilayer increases, polar phospholipid headgroups reorient in order to provide more coverage per headgroup for the increasing fraction of cholesterol molecules, as drawn in Fig. 10 b. The headgroup umbrellas are “stretched” to provide more coverage area."<br /><br />They are talking about reorienting and stretching. In principle one can imagine headgroup stretching and/or reorientation leading to the umbrella effect sketched in Fig. 10 in the original paper without tilting. Even more imagination is needed to figure out reorientation or stretching which would leave the alpha and beta order parameters practically unchanged, as observed in experiments. <br /><br />Maybe we could avoid the word tilting and write:<br /><br />"For example, it has been suggested that the surrounding lipids shield cholesterol from interactions with water by reorienting their head groups (“umbrella model”) [114]"Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-32918881764890433052015-01-12T11:31:48.318+02:002015-01-12T11:31:48.318+02:00Note that, if I understand correctly the simulatio...Note that, if I understand correctly the simulation details given above by Alexandru, in Table 1 we should write t_sim(ns) = 50 and t_anal(ns) = 20.markus.https://www.blogger.com/profile/05973383391755193687noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-38291609609750551772015-01-12T10:27:09.039+02:002015-01-12T10:27:09.039+02:00I've got one comment on the text. At the momen...I've got one comment on the text. At the moment the manuscript says:<br /><br />"For example, it has been suggested that the surrounding lipids shield cholesterol from interactions with water by tilting their head groups (“umbrella model”)"<br /><br />However, the original umbrella model paper does not mention that some tilting of head groups is required for the umbrella effect. I don't know if this idea has surfaced due to the simulation results but somehow the text should be adapted a bit to emphasise the origins of the tilting idea.<br />Matti Javanainenhttps://www.blogger.com/profile/13300446060709340277noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-52458751188179759562015-01-11T13:56:24.988+02:002015-01-11T13:56:24.988+02:00Hi,
Here are the details of CHARMM36UA simulation...Hi,<br /><br />Here are the details of CHARMM36UA simulations.<br /><br />Input files are available http://dx.doi.org/10.5281/zenodo.13821 .<br /><br />Values for Table 1:<br /><br />CHARMM36-UA [87, 88] DLPC 128 3840 323 30 20 [http://dx.doi.org/10.5281/zenodo.13821] SI<br /><br />Simulation details:<br /><br />A hydrated bilayer consisting of 128 DLPC lipids and 3840 water molecules is modeled by the force field of Lee and co-workers [88], which is a combination of the all-atom CHARMM36 force-field and the united-atom Berger model. The nonbonding interactions are calculated using an atom-based switching function with inner and outer cutoffs of 0.8 and 1.2 nm [88]. Long range electrostatic interactions are implemented using the particle-particle particle-mesh solver with a relative accuracy of 0.0001. The system is first equilibrated for 30 ns in the NP$\gamma$T ensemble (Nose-Hoover style thermostat and barostat with anisotropic pressure coupling) at 323 K and 1 bar with timestep of 1 fs, the next 20 ns of dynamics are taken for calculation of configurational averages. Simulations were carried out by using the LAMMPS package ( http://doi.org/10.1006/jcph.1995.1039 ), the input files are available ( http://dx.doi.org/10.5281/zenodo.13821 ).Anonymoushttps://www.blogger.com/profile/00656662181573495590noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-70400863446365011112015-01-11T13:07:15.931+02:002015-01-11T13:07:15.931+02:00Thanks for the feedback.
-> Samuli's comme...Thanks for the feedback.<br /><br />-> Samuli's comment:<br />I agree with your changes to the text. I've made an account on Zenodo and will upload the trajectories there next week, so that I'll be able to add permanent links in the PDF and will finally upload that PDF on Zenodo as well. It's better to upload everything on Zenodo since I'm not sure my web-page URL will be active in, say, 10 years. Will make you know once done.<br />Finally, I see that we do not cite the ref of SPC that is first encountered in Poger et al. section, but mentionned again in Kukol section. Shall we cite the ref (Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces; Pullman, B., Ed.; Reidel Publishing Company: Dordrecht, The Netherlands, 1981, pp 331-342.)? I also noticed we don't have cited the generalized reaction field ref. I suggest to add the ref (http://dx.doi.org/10.1063/1.469273) at the end of the sentence "For the former the generalized reaction field (RF) with a dielectric permitivity of 62 was used beyond the 1.4 nm cutoff."<br /><br /><br />-> Markus' comment #1:<br />You're right it's important to mention this story of dihedral. <br />After the sentence "The initial hydrated bilayer structure of 128 DPPC/5841 water molecules as well as force field parameters were downloaded from David Poger’s web site (http://compbio.chemistry.uq.edu.au/~david/) on April 2012." I suggest to add the following:<br />---<br />We noticed that the same files downloaded in October 2013 appear to lack two dihedral angles in the choline headgroup (only one dihedral of type gd_29 allowing the rotation of the 3 choline methyls) compared to the April 2012 version (3 dihedrals of type gd_29 for the 3 choline methyls). This should not affect the bilayer structure and only change the kinetics of the choline methyls rotation, however the October 2013 version has not been tested.<br />---<br /><br />-> Markus' comment #2:<br />Good suggestion to mention about the two clones of simulations for each condition (RF and PME). I agree with your proposition to change Table 1 and SI. I'll upload the 4 trajectories on Zenodo and will make you know once done.<br />Anonymousnoreply@blogger.com