tag:blogger.com,1999:blog-1283194685237019772.post4952965143427982656..comments2024-03-26T17:11:28.045+02:00Comments on The NMRlipids Project: NMRlipids IV: First draft of the manuscript about PS lipids markus.http://www.blogger.com/profile/05973383391755193687noreply@blogger.comBlogger29125tag:blogger.com,1999:blog-1283194685237019772.post-36710604485455997842019-01-16T22:39:09.466+02:002019-01-16T22:39:09.466+02:00Thanks, it looks good to me now.Thanks, it looks good to me now.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-968078814495718342019-01-10T15:05:15.469+02:002019-01-10T15:05:15.469+02:00Dear Samuli, I have updated the figures. Are they ...Dear Samuli, I have updated the figures. Are they good now?Anonymoushttps://www.blogger.com/profile/08217361776415663315noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-29629781367678915432019-01-02T14:23:24.818+02:002019-01-02T14:23:24.818+02:00Thanks again. I made a new version of the figure: ...Thanks again. I made a new version of the figure: https://github.com/NMRLipids/NMRlipidsIVotherHGs/blob/master/Figs/structures-eps-converted-to.pdf<br /><br />The atom labels in the left column are now too small. Could you make new versions of figures titled chol.png and pc_hg.png in your drive having atom labels with larger font? Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-83893514743108681442018-12-26T17:12:19.263+02:002018-12-26T17:12:19.263+02:00Dear Samuli, sorry for the late reply.
Please fin...Dear Samuli, sorry for the late reply.<br /><br />Please find labeling figures via link:<br />https://drive.google.com/drive/folders/1_cbzmtmGtNcclCr2wb4Ex8o3ptV4ffH2?usp=sharingAnonymoushttps://www.blogger.com/profile/08217361776415663315noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-27999211194387938922018-11-21T14:54:14.156+02:002018-11-21T14:54:14.156+02:00I have now composed a new figure summarizing the m...I have now composed a new figure summarizing the most essential conformations for the manuscript and included this into the manuscript and updated the discussion: <br />https://github.com/NMRLipids/NMRlipidsIVotherHGs/blob/master/Figs/structures-eps-converted-to.pdf<br /><br />I think that we still need a figure with atom labels for the b) part of this figure. Would it be possible to make similar labelling figure for b) as in the part a)? Maybe it would be also possible to have this kind of figure with high resolution?<br /><br />Other figures are now in the SI but are referred in the text.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-11203302461426512712018-11-06T20:29:56.942+02:002018-11-06T20:29:56.942+02:00I have added the figures for the headgroup to. Ple...I have added the figures for the headgroup to. Please find it via link:<br />https://drive.google.com/open?id=1_cbzmtmGtNcclCr2wb4Ex8o3ptV4ffH2Anonymoushttps://www.blogger.com/profile/08217361776415663315noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-6304441151480759252018-11-02T11:48:16.892+02:002018-11-02T11:48:16.892+02:00Thanks. Could you also make a figure about the hea...Thanks. Could you also make a figure about the headgroup part, i.e., from the figure presenting the figS7PC? This would be actually more interesting when comparing PC and PS.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-78031929332291087982018-11-01T20:40:47.057+02:002018-11-01T20:40:47.057+02:00Dear Samuli,
I have added structural figures for ...Dear Samuli,<br /><br />I have added structural figures for glycerol backbone (figS8_POPC at https://drive.google.com/open?id=1_cbzmtmGtNcclCr2wb4Ex8o3ptV4ffH2). It represents the differences in the distributions (figS6PC) between Slipids POPC and POPS lipids.Anonymoushttps://www.blogger.com/profile/08217361776415663315noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-51747468856638819312018-10-30T17:55:02.698+02:002018-10-30T17:55:02.698+02:00I have changed the names.
For the dashed lines, I...I have changed the names.<br /><br />For the dashed lines, I did not account for different number of calculated angles for PC and PS lipids. Now should be ok.<br /><br />Please find plots via link:<br />https://drive.google.com/open?id=1_cbzmtmGtNcclCr2wb4Ex8o3ptV4ffH2<br />Anonymoushttps://www.blogger.com/profile/08217361776415663315noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-87248921364675121852018-10-29T22:56:41.977+02:002018-10-29T22:56:41.977+02:00Thanks for the results.
Should the label for the...Thanks for the results. <br /><br />Should the label for the green dashed line be "POPC, Slipids"?<br /><br />The dashed lines in the figS6PC are the same for each dihedral.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-26973812378159204292018-10-29T15:50:26.199+02:002018-10-29T15:50:26.199+02:00Dear Samuli,
I have plotted figures analogous to S...Dear Samuli,<br />I have plotted figures analogous to S6 and S7 for POPC lipids. Please find them via link (figS6PC, figS7PC):<br />https://drive.google.com/open?id=1_cbzmtmGtNcclCr2wb4Ex8o3ptV4ffH2<br /><br />There are some differences in distributions for PC and PS headgroups. Thus, I will plot structures soon.Anonymoushttps://www.blogger.com/profile/08217361776415663315noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-13415167595295525632018-10-28T20:09:23.011+02:002018-10-28T20:09:23.011+02:00Dear Samuli,
1. I have reworked figures S6 and S7....Dear Samuli,<br />1. I have reworked figures S6 and S7. Now both lines seem to be visible. Please find them via link:<br />https://drive.google.com/open?id=1_cbzmtmGtNcclCr2wb4Ex8o3ptV4ffH2<br />2. Regarding the POPC trajectories, I will do this during this week. Hopefully, by Tuesday.Anonymoushttps://www.blogger.com/profile/08217361776415663315noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-2011709939266889072018-09-18T13:47:30.145+03:002018-09-18T13:47:30.145+03:00These results are now added in the figure: https:/...These results are now added in the figure: https://github.com/NMRLipids/NMRlipidsIVotherHGs/blob/master/Figs/CHANGESwithMONVALENTwithPS-eps-converted-to.pdf<br /><br />There is also a new post discussing about the evaluation of counterion binding affinity to PS containing bilayers: http://nmrlipids.blogspot.com/2018/09/nmrlipids-iv-challenges-in-evaluating.htmlSamuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-79020621933247592042018-09-17T14:15:25.528+03:002018-09-17T14:15:25.528+03:00Dear Pavel,
thanks again for the update. I have no...Dear Pavel,<br />thanks again for the update. I have now included the new figures and updated the discussion in the manuscript. <br /><br />Two more questions:<br />1) The dihedral distributions from CHARMM36 and CHARMM36UA seem to overlap almost perfectly. Is this correct? If yes, maybe the line for CHARMM36 should be slightly thicker to make it visible. Now it is quite difficult to distinguish from some figures<br />2) Would it be possible to make similar figures (snapshots and headgroup dihedral distributions) from CHARMM36 and Slipids POPC trajectories, available from http://doi.org/10.5281/zenodo.153944 and http://doi.org/10.5281/zenodo.166034, respectively? I think that the differences between headgroup order parameters of POPC and POPS are roughly reproduced by these models, thus we could consider using these to look at the structural differences.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-45831645329799700122018-09-07T19:26:30.865+03:002018-09-07T19:26:30.865+03:00Dear Samuli,
I have reworked the figures as you as...Dear Samuli,<br />I have reworked the figures as you asked. As for the question 4 - there was a problem with my script. Now everything is ok. Please, find new figures here:<br />https://drive.google.com/open?id=1_cbzmtmGtNcclCr2wb4Ex8o3ptV4ffH2Anonymoushttps://www.blogger.com/profile/08217361776415663315noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-16622103709237136712018-09-07T13:39:57.351+03:002018-09-07T13:39:57.351+03:00These are now included in the manuscript.These are now included in the manuscript.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-32448646506916772922018-09-05T14:42:21.852+03:002018-09-05T14:42:21.852+03:00And here are the data for the same membranes with ...And here are the data for the same membranes with CaCl2.<br />https://doi.org/10.5281/zenodo.1409551<br />Matti Javanainenhttps://www.blogger.com/profile/13300446060709340277noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-45632359565143668122018-08-27T13:07:26.749+03:002018-08-27T13:07:26.749+03:00I generated starting configurations for the PC/PS ...I generated starting configurations for the PC/PS simulations using CHARMM-GUI and rerun the mixtures with KCl. These simulations should have the correct stereoisomer. The new data are included in the old Zenodo DOI: 10.5281/zenodo.1404040. The data with CaCl_2 will follow once the ion binding has converged. The salt-free system will also be included in the CaCl_2 upload.Matti Javanainenhttps://www.blogger.com/profile/13300446060709340277noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-56922971883174237142018-08-17T16:26:41.475+03:002018-08-17T16:26:41.475+03:00I have now started simulations of POPC:POPS (5:1) ...I have now started simulations of POPC:POPS (5:1) mixture with additional amount of NaCl and KCl counterions, which were requested in todo point 4. Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-1735745695356798682018-08-16T14:35:01.880+03:002018-08-16T14:35:01.880+03:00I have rewritten the discussing about conformation...I have rewritten the discussing about conformations and dihedrals, and pushed it into the current manuscript in GitHub. For the headgroup, it is now proposed that the rigid C_alpha-C_beta-C_gamma-O_gamma dihedral in CHARMM36 and Slipid is more realistic than more flexible structures in other models. There is also some discussion about N-C_beta-C_aplha-O_alpha dihedral. Conclusions from the glycerol backbone would require some more elaborate analysis.<br /><br />I still have few requests about the pictures:<br />1) Could you swap the order in figS8.png such that the headgroup structures would be on top and glycerol backbone structures on bottom? This would be more fluent with the discussion in the manuscript.<br />2) There is a typo in the labeling of "Brger" in S6 and S7.<br />3) GROMOS-CKP2 model is labeled twice. Note that the current naming convention of CKP models is described in the caption of Table 1.<br />4) N-C_beta-C_alpha-O_alpha dihedral seems very similar for CHARMM36 and CHARMM36ua in the figS8.png. However, maximum at 60 degrees seems to be missing from the CHARMM36ua results in Fig. S6. Do you have any idea what could be the reason for this?<br />5) Higher resolution version of figure PS_Labels.png would be useful.<br />Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-71163865456873693282018-08-14T14:41:21.501+03:002018-08-14T14:41:21.501+03:00Matti Javanainen gave me a preliminary trajectory ...Matti Javanainen gave me a preliminary trajectory from POPC:POPS (5:1) simulation with the fixed itp file by Tom Piggot. I compared the POPS order parameter results to the ones from POPC:OPPS (5:1):<br />https://github.com/NMRLipids/NMRlipidsIVotherHGs/blob/master/scratch/MACROGcomp.png<br /><br />The results are quite similar, in contrast to the previous comparison of pure POPS simulations which gave significant differences between the models:<br />https://github.com/NMRLipids/NMRlipidsIVotherHGs/blob/master/Figs/HGorderparametersPOPSvsOPPS-eps-converted-to.pdf<br /><br />This suggested that the problem would be in the initial conformations, as also indicated by Tom Piggot above. Therefore, we took a look to initial configurations with Matti Javanainen and noticed that the starting configuration shared by the MacRog developers has the serine in D-stereoisomer,<br /> while other models have the L-stereoisomer. The latter is present in biological systems.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-60108314723370391962018-08-14T00:10:41.799+03:002018-08-14T00:10:41.799+03:00I will double check the two topologies to check th...I will double check the two topologies to check there isn't anything different here but I'm pretty confident there won't beThomas Piggothttps://www.blogger.com/profile/14030778642272576601noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-43133237847866779572018-08-13T23:58:04.514+03:002018-08-13T23:58:04.514+03:00I think this could well be due to the use of diffe...I think this could well be due to the use of different starting structures in these two simulations (like that seen previously with the OPLS-UA Ulmschneider PC simulations). My simulations with the PO tails were started from the same membrane structure as all of other POPS simulations I did. This structure was originally a CHARMM36 POPS membrane made using the CHARMM-GUI.Thomas Piggothttps://www.blogger.com/profile/14030778642272576601noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-57153740485198516742018-08-13T14:04:14.048+03:002018-08-13T14:04:14.048+03:00Thanks again. Now I am comparing the new and previ...Thanks again. Now I am comparing the new and previous versions of the figS8.png.<br /> <br />The orientation of the headgroup snapshots from MacRog in the previous version seems to be somehow different than in other models: https://github.com/NMRLipids/NMRlipidsIVotherHGs/blob/master/Figs/figS8.png<br /><br />In the new version the orientation seems to be similar to the other models:<br />https://drive.google.com/drive/folders/1_cbzmtmGtNcclCr2wb4Ex8o3ptV4ffH2<br /><br />In addition, the headgroup dihedral distributions from MacRog in the new and previous plots seems to be different, even thought the force field should be identical in this region: https://github.com/NMRLipids/NMRlipidsIVotherHGs/issues/16<br /><br />Maybe Tom Piggot or Matti Javanainen could also have some insight in this?<br />Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-32936250093338546282018-08-12T00:41:48.867+03:002018-08-12T00:41:48.867+03:00Dear Samuli,
I have reworked the figures for the n...Dear Samuli,<br />I have reworked the figures for the new labeling and correct MacRog trajectory. Please find new versions here:<br />https://drive.google.com/open?id=1_cbzmtmGtNcclCr2wb4Ex8o3ptV4ffH2<br /><br />For the analysis I used the trajectories POPS/Na+ for CHARMM36, CHARMM36UA, Slipids, Berger, MacRog, GROMOS-CKPM, GROMOS-CKP, Lipid17/JC, Lipid17/ff99 from Table1 of the manuscript.Anonymoushttps://www.blogger.com/profile/08217361776415663315noreply@blogger.com