tag:blogger.com,1999:blog-1283194685237019772.comments2024-03-14T15:34:26.853+02:00The NMRlipids Projectmarkus.http://www.blogger.com/profile/05973383391755193687noreply@blogger.comBlogger850125tag:blogger.com,1999:blog-1283194685237019772.post-4703084799504101912022-08-31T14:15:18.096+03:002022-08-31T14:15:18.096+03:00I did more careful analysis on the size dependence...I did more careful analysis on the size dependence of form factors and order parameters using the recent dataset containing simulations in different box sizes and cholesterol concentrations: https://doi.org/10.5281/zenodo.5767450<br /><br />The results can be found from here: https://raw.githubusercontent.com/NMRLipids/DataBankManuscriptText/main/Figures/SizeDependence.pdf<br /><br />Indeed, the lobe heights seem to decrease with increasing simulation box size. This seems to be related to the reduced peak heights in the electron density profiles. Nevertherless, the locations of form factor minima and order parameters are practically independent on the simulation box size.<br /><br />In conclusion, using the full form factor in the quality evaluation (as currently done) makes the quality dependent on the simulation box size. Therefore, a quality measure focusing on locations of form factor minima would be probably better. I am currently investigating different options for this.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-47750615785330902252022-05-30T14:49:06.181+03:002022-05-30T14:49:06.181+03:00I think I included the sim2exp version to the slid...I think I included the sim2exp version to the slides in Berlin. However, including simulation error in this formula is quite easy. Now xi^2 essentially gives the difference between the simulated and experiment in the "units" of experimental error. To convert the scaling to experimental+simulation error one could just replace delta_Fe with delta_Fe+delta_Fs in the xi^2 formula.<br /><br />I have not checked how the size effect is with other system sizes and if it seems to saturate at some point. As Samuli said, it would be useful to do this analysis from the databank. <br /><br />As I said above, the minima are unaffected by the size so indeed it seems (luckily) unlikely that the strong correlation of the minima with the membrane properties is obscured by the possible simulation size effect.Hannehttps://www.blogger.com/profile/05160906501508849933noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-53408973860941966762022-05-28T23:17:36.093+03:002022-05-28T23:17:36.093+03:00I do not remember such equation and do not find it...I do not remember such equation and do not find it from the notes that I have: https://raw.githubusercontent.com/NMRLipids/MATCH/master/scripts/NMRL3_analysis/qualitymeas.pdfSamuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-90201333233357486562022-05-28T13:35:48.910+03:002022-05-28T13:35:48.910+03:00Samuli wrote: "The form factor quality estima...Samuli wrote: <i>"The form factor quality estimator is currently taken directly from the SIMtoEXP and the simulation error is not there, so it is not in our equation either. If we would include it, would you have an idea how to do it exactly?"</i><br /><br />If I recall correctly, Hanne proposed an equation for this already in the NMRlipids2019 workshop in Berlin? Hanne, do you still remember how it was? Or Samuli, do you maybe still have the notes of what was proposed?markus.https://www.blogger.com/profile/05973383391755193687noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-4774876311240469512022-05-25T08:16:39.774+03:002022-05-25T08:16:39.774+03:00Hi! I have recently run some simulations with the ...Hi! I have recently run some simulations with the OPLS3e force field, and it reproduces all the POPC order parameters quite well. Thus it might be a useful addition to the first Databank publication? The Zenodo DOI-links are:<br /><br />10.5281/zenodo.6342807<br />10.5281/zenodo.6345186<br />10.5281/zenodo.6345702<br /><br />10.5281/zenodo.6345780<br />10.5281/zenodo.6355375<br />10.5281/zenodo.6361140<br /><br />10.5281/zenodo.6361725<br />10.5281/zenodo.6363524<br />10.5281/zenodo.6364216<br /><br />10.5281/zenodo.6364498<br />10.5281/zenodo.6365067<br />10.5281/zenodo.6366287<br /><br />10.5281/zenodo.6345943<br />10.5281/zenodo.6346717<br />10.5281/zenodo.6347738<br /><br />10.5281/zenodo.6347982<br />10.5281/zenodo.6578036<br />10.5281/zenodo.6350600<br /><br />10.5281/zenodo.6350923<br />10.5281/zenodo.6351089<br />10.5281/zenodo.6351349<br /><br />10.5281/zenodo.6352681<br /><br /><br />Best regards,<br />Milla Lindström,<br />University of Eastern Finland<br />Milla Lindströmhttps://www.blogger.com/profile/02120151021216096909noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-75294293116581187402022-05-24T15:39:46.502+03:002022-05-24T15:39:46.502+03:00Hello,
I think at the moment it would be useful f...Hello,<br /><br />I think at the moment it would be useful for us to try to get our simulations running on OpenMM as well. While looking into this, I have found the Li parameters already available in OpenMM format (https://github.com/Inniag/openmm-scripts-amoeba/). I unfortunately do not have a working experience with OpenMM. Would anyone be interested in creating the simulation input files with OpenMM?Batuhan Kavhttps://www.blogger.com/profile/16276244213761216101noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-12534255491635542262022-05-24T14:12:44.012+03:002022-05-24T14:12:44.012+03:00About the system size, 34 lipids is quite a bit sm...About the system size, 34 lipids is quite a bit smaller than typical simulations. Have you checked whether there is size dependency when comparing only systems with more than 100 lipids for example? I have been looking correlations between form factor minima, area per lipid, thickness and membrane order, and the minima seems to correlate well with membrane properties, see https://github.com/NMRLipids/DatabankExercises/blob/master/APL/correlations.pdf and https://github.com/NMRLipids/DatabankExercises/blob/master/APL/AreaPerLipidAndThicknessExamples.ipynb <br /><br />It might be useful to try to figure out from the NMRlipids databank if lobe heights correlate with some membrane properties.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-70321156326972395142022-05-23T08:56:49.297+03:002022-05-23T08:56:49.297+03:00The form factor quality estimator is currently tak...The form factor quality estimator is currently taken directly from the SIMtoEXP and the simulation error is not there, so it is not in our equation either. If we would include it, would you have an idea how to do it exactly?<br /><br />Adding errors to plots is a good idea. Currently the code does not print the error, but I can take a look if we could do it. I am currently updating the code to work properly for united atom systems and systems with periodic jumps in z-direction.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-39464169232296468402022-05-20T17:13:08.172+03:002022-05-20T17:13:08.172+03:00Additional reminder that the (relative) form facto...Additional reminder that the (relative) form factor lobe heights seem to be fairly sensitive to the system size. I just calculated a comparison of C36 and Slipids form factors from small (34 lipids) and big (200 lipids) simulations and scaled the first lobes to be identical for the different system sizes: <br />https://github.com/hsantila/FormFactor_data/blob/main/Slipids_C36.png<br /><br />A quality estimator were significant amount of comparison point are on the lobes is very much affected by finite size effect. Conversely, the minima and maxima location in q-axis are fairly insensitive. A quick fix might be heuristically limiting the q-range where the comparison is performed?Hannehttps://www.blogger.com/profile/05160906501508849933noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-25115658489487247612022-05-20T11:43:50.555+03:002022-05-20T11:43:50.555+03:00Looks amazing! You and Anne have done very nice jo...Looks amazing! You and Anne have done very nice job with this.<br /><br />I would still consider taking account the errors in the form factors too since they are accounted for the order parameters. <br />If you definitely do not want to add them to the quality estimator, they would be nice to have at least the plots so one can visually asses the overlap with the experimental data and where the curves are most accurate. <br /><br />Error bars should be an easy addition to the code if you calculate the form factors averaging the frame-vise form factors.<br /><br />Having now found several caveats in the converge and calculation of the form factors, I have trouble trusting any curves published in the litterature. It would sense to do this with care once an for all for the databank.<br /><br />BR<br /><br />Hanne<br /> Hannehttps://www.blogger.com/profile/05160906501508849933noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-11154694302097565412022-02-11T21:38:14.657+02:002022-02-11T21:38:14.657+02:00If dipole convergence issue occurs right away, the...If dipole convergence issue occurs right away, the structure or prm files are probably problematic. If it happens after a while, check the biomol utexas page for options. The latest Tinker9 should be very stable regarding the dipole scg. Atomic Force (Ren)https://www.blogger.com/profile/04881886194544089562noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-892675750542828932022-02-11T10:36:34.847+02:002022-02-11T10:36:34.847+02:00Regarding the semi-isotropic pressure coupling, I ...Regarding the semi-isotropic pressure coupling, I already contacted the developers <br /><br />https://github.com/TinkerTools/tinker9/issues/181<br /><br />For the POPE lipids, the C2 order parameter for the SN-1 chain has an error in the original publication. However, the other tail group order parameters, as I remember, were reproducible. Batuhan Kavhttps://www.blogger.com/profile/16276244213761216101noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-91199612859927685352022-02-11T10:27:05.327+02:002022-02-11T10:27:05.327+02:00Hello,
Thank you for the information, Blake.
I ...Hello,<br /><br />Thank you for the information, Blake. <br /><br />I tried the POPE system with the Langevin barostat. I have tried different time steps from 0.1 to 2 fs but all crashed with induced dipoles not converging. Did you have similar issues before? Batuhan Kavhttps://www.blogger.com/profile/16276244213761216101noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-65522320216243473012022-02-10T18:48:07.040+02:002022-02-10T18:48:07.040+02:00Yes it can run anisotropic (ANISO-PRESSURE will al...Yes it can run anisotropic (ANISO-PRESSURE will allow anisotropic relaxation). I suggest asking questions on https://github.com/TinkerTools/tinker9 (issues). We will all see it.Atomic Force (Ren)https://www.blogger.com/profile/04881886194544089562noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-18969190908977264712022-02-10T18:15:38.253+02:002022-02-10T18:15:38.253+02:00You're more than welcome. I'll have to rea...You're more than welcome. I'll have to reach out the Tinker9 developers about the ability to run anisotropic or semi-isotropic (the documentation is something I'm trying to contribute to as well, as it's pretty sparse). I need to go back and look at my data -- I've been benchmarking the systems with both Nose-Hoover and Langevin barostats (NH requires a 1 fs timestep, which is unfortunate). The DMPC system I mentioned that is stable was run with the NH, so I hope I didn't speak too soon. I do question the published results -- the DMPC system I've simulated severely underestimates the 2H NMR order parameters for most of the acyl tail, from C2 to C11, compared to experimental results.Blakehttps://www.blogger.com/profile/06294766024470123515noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-19856633582508361352022-02-10T17:57:04.742+02:002022-02-10T17:57:04.742+02:00Thanks for the information!
Did you use anisotrop...Thanks for the information!<br /><br />Did you use anisotropic pressure scaling? I think that I had problems to use it with other than Berendsen barostat in Tinker9. Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-50129266793647309882022-02-10T17:25:17.506+02:002022-02-10T17:25:17.506+02:00We are not associated with the lipid parameters pu...We are not associated with the lipid parameters published by Li. It is in AMOEBA style but we do not distribute them with AMOEBA parameter files in anyway. I won't be surprised they need to be worked on/improved (all parameters straightly came out of QM of small fragments). We only did some limited tests with them so far. There are issues but haven't seen gel. We plan to work on an AMOEBA lipid library with Blake (see his comments below). -Pengyu RenAtomic Force (Ren)https://www.blogger.com/profile/04881886194544089562noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-12458981542114466772022-02-10T17:12:16.102+02:002022-02-10T17:12:16.102+02:00Batuhan,
I've been working on reproducing th...Batuhan, <br /><br />I've been working on reproducing the results from the Li parameters as part of my sabbatical project for the past 18 months. I've been running DMPC simulations in both Tinker8-OpenMM and Tinker9, which has the langevin barostat included. This may do a better job of treating the system, as I don't see any transition to the gel phase upon visual inspection (am calculating the area per lipid this week). I would be interested in participating in the Zoom discussion when it happens, as I have a vested interest in seeing a polarizable lipid force field be successful (we want to use it for the protein systems we are investigating). You can get in touch with me at blake.mertz@mail.wvu.edu. Thanks for taking on this project, it is an ambitious one!<br /><br />BlakeBlakehttps://www.blogger.com/profile/06294766024470123515noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-73400233098396723832022-02-10T09:26:54.769+02:002022-02-10T09:26:54.769+02:00Thanks for the comment.
Indeed, we have been able...Thanks for the comment.<br /><br />Indeed, we have been able to run AMOEBA using Tinker9 on GPUs directly with a decent performance. What is missing thought is the semi-isotropic pressure coupling which would be optimal for lipid bilayers. Nevertheless, I think that the fully anisotropic is ok as long as the system does not explode. <br /><br />The problem in our simulations with Tinker9 is that they go to gel-like phase, while AMOEBA lipid bilayer simulations with OpenMM in correct phase has been reported in the literature in the publications cited in the original post. Question is now if this is due to the parameters we have or some algorithms used. Personally I would guess the parameters, but it would be really good to exclude the possibility of algorithm.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-91838104129649432912022-02-10T00:49:08.895+02:002022-02-10T00:49:08.895+02:00Thank you for the contribution.
Please note that ...Thank you for the contribution.<br /><br />Please note that we would strongly encourage that "all communications would be written such that they are assignable to a person and affiliation", see the post <a href="http://nmrlipids.blogspot.com/2013/07/on-credits.html" rel="nofollow">On credits</a>.markus.https://www.blogger.com/profile/05973383391755193687noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-80873883126996829662022-02-10T00:30:58.334+02:002022-02-10T00:30:58.334+02:00You can run AMOEBA simulations using Tinker9 on GP...You can run AMOEBA simulations using Tinker9 on GPUs directly. Same Tinker (CPU) input files. It has the (best) Langevin piston pressure control.<br />https://github.com/TinkerTools/tinker9<br />https://biomol.bme.utexas.edu/tinkergpu/index.php?title=Tinkergpu:Tinker-tut#How_to_run_Tinker9_using_GPU_(2021)Atomic Force (Ren)https://www.blogger.com/profile/04881886194544089562noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-28962080071408914792021-12-22T09:47:24.304+02:002021-12-22T09:47:24.304+02:00The current codes form factor calculation codes de...The current codes form factor calculation codes developed based on work of group 1 are now in here:<br />https://github.com/NMRLipids/Databank/blob/main/Scripts/BuildDatabank/FormFactors.py<br />https://github.com/NMRLipids/Databank/blob/main/Scripts/BuildDatabank/form_factor.py<br /><br />The results can be found from the folders in:<br />https://github.com/NMRLipids/Databank/blob/main/Scripts/BuildDatabank/form_factor.py<br /><br />However, some further testing of the accuracy of the code is still going on.Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-71369314741203176662021-12-22T09:41:15.512+02:002021-12-22T09:41:15.512+02:00The quality evaluation for order parameters is now...The quality evaluation for order parameters is now implemented roughly as proposed by group 1. More details are presented in the presentation given in online meeting on 17.12.2021: https://github.com/NMRLipids/DatabankExercises/blob/master/Presentations/DataBankPresentation2021.pdf<br /><br />Simulation rankings based on the current quality evaluations are shown in Jupyter notebook: https://github.com/NMRLipids/Databank/blob/main/Scripts/AnalyzeDatabank/plotQuality.ipynbSamuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-74572437984316476592021-10-13T10:41:57.340+03:002021-10-13T10:41:57.340+03:00The new format for storing the compositions of sys...The new format for storing the compositions of systems proposed by group 3 is now implemented in the databank. The instructions to make info files is updated accordingly: https://github.com/NMRLipids/Databank/blob/main/Scripts/BuildDatabank/info_files/README.md<br /><br />Analysis script using the new format are significantly simpler than before, see for example:<br />Area per lipid: <br />https://github.com/NMRLipids/Databank/blob/main/Scripts/AnalyzeDatabank/calcAPL.py<br />Order parameters: <br />https://github.com/NMRLipids/Databank/blob/main/Scripts/AnalyzeDatabank/calcOrderParameters.py<br />Statistics: <br />https://github.com/NMRLipids/Databank/blob/main/Scripts/AnalyzeDatabank/databank_dict.ipynbSamuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.comtag:blogger.com,1999:blog-1283194685237019772.post-68837800860151041022021-08-18T13:26:02.488+03:002021-08-18T13:26:02.488+03:00The manuscript is now published in the Journal of ...The manuscript is now published in the Journal of American Chemical Society with the updated title: Inverse Conformational Selection in Lipid–Protein Binding (https://doi.org/10.1021/jacs.1c05549). Samuli Ollilahttps://www.blogger.com/profile/06106569992787533569noreply@blogger.com