tag:blogger.com,1999:blog-1283194685237019772.post5501561530187325020..comments2024-03-26T17:11:28.045+02:00Comments on The NMRlipids Project: NMRlipids IV: Challenges in evaluating counterion binding affinity to PS bilayersmarkus.http://www.blogger.com/profile/05973383391755193687noreply@blogger.comBlogger8125tag:blogger.com,1999:blog-1283194685237019772.post-81499834125471173852018-10-31T19:36:01.561+02:002018-10-31T19:36:01.561+02:00Thanks. I have red this quite carefully. My unders...Thanks. I have red this quite carefully. My understanding is that their conclusions about binding details of calcium to PS headgroup relies quite heavily on CHARMM36 simulations with the NBfix for the calcium, which gives too weak binding affinity according to our results.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-29922735460702307342018-10-17T17:23:23.379+03:002018-10-17T17:23:23.379+03:00I'm not part of the PS project, but I just saw...I'm not part of the PS project, but I just saw this new paper in BJ that might be of interest to you guys: https://doi.org/10.1016/j.bpj.2018.08.044.Patrick Fuchshttps://www.blogger.com/profile/16910815195856162826noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-67721521906261786982018-10-02T22:31:22.203+03:002018-10-02T22:31:22.203+03:00I have added the density profiles now in the figur...I have added the density profiles now in the figures:<br />https://github.com/NMRLipids/NMRlipidsIVotherHGs/blob/master/Figs/CIdensPSOCmixt-eps-converted-to.pdf<br />https://github.com/NMRLipids/NMRlipidsIVotherHGs/blob/master/Figs/CAdensPCPSmixture-eps-converted-to.pdf<br /><br />I have three issues in mind:<br />1) The density values are somewhat different than in the results from other simulations. Based on the filenames these should be the number densities. Maybe you could specify the units?<br />2) The density profiles from KCl and NaCl simulations look little bit strange (I did not plot the 2M, 3M and 4M results for clarity). As far as I know, the ion parameters used here are prone to cluster. Have you checked that there is no clustering of ions in the solution? This could also explain the slightly weird order parameter results from these systems.<br />3) I could not find the density profiles from mixtures with only sodium or potassium counterions. Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-23980458405187526172018-10-02T17:11:18.629+03:002018-10-02T17:11:18.629+03:00Task 3 is completed, and the data is uploaded to g...Task 3 is completed, and the data is uploaded to github.Batuhan Kavhttps://www.blogger.com/profile/16276244213761216101noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-52014727943584706062018-09-28T19:46:23.051+03:002018-09-28T19:46:23.051+03:00When plotting the results from your commit (https:...When plotting the results from your commit (https://github.com/NMRLipids/NMRlipidsIVotherHGs/commit/141a1b4fbbae8d657ea87590de864ed02c58c0a2), I noticed a large difference between the results from Dang and ff99 (Åqvist) ions, which could also come from the difference between Amber and Gromacs programs, see issue https://github.com/NMRLipids/NMRlipidsIVotherHGs/issues/21Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-7134117721221017282018-09-27T16:59:17.141+03:002018-09-27T16:59:17.141+03:00This data is now analyzed and the potassium densit...This data is now analyzed and the potassium density profile and area per molecule are in figure:<br />https://github.com/NMRLipids/NMRlipidsIVotherHGs/blob/master/Figs/NAdensPOPS-eps-converted-to.pdf<br /><br />As expected in the discussion in this post, the potassium counterion binding is weakest among the tested models. Notably, the area per molecule is substantially higher in simulations with potassium counterions and agrees with the experimental value. Also, the headgroup order parameters are different with potassium counterions: https://github.com/NMRLipids/NMRlipidsIVotherHGs/blob/master/Figs/HGorderparametersPS.pdfSamuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-35397704685516957002018-09-25T22:11:19.621+03:002018-09-25T22:11:19.621+03:00Task 1 is completed, and the data is available at:...Task 1 is completed, and the data is available at: https://doi.org/10.5281/zenodo.1434990Matti Javanainenhttps://www.blogger.com/profile/13300446060709340277noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-54647679989465923252018-09-19T12:21:08.415+03:002018-09-19T12:21:08.415+03:00To the point number 2. -- I will do the simulation...To the point number 2. -- I will do the simulations with Lipid14 at 298 K.<br />I have the configurations so it is relatively easy for me to run them. Josef Melcrhttps://www.blogger.com/profile/12422047696918877379noreply@blogger.com