On Mon, May 8, 2023 at 12:44 PM Cecília Álvares <[email protected]> wrote:
> Hey Marvin, > > It seems to have worked! I guess it was not very intelligent of me to have > taken for granted that my previous setup for the scaling factor was > correct: if I had compared the results with vs without my factor instead of > analyzing it isolate to see if the problem had been solved, I would have > noted long ago that there the factor setup was not on and saved some time > and energy :"D > > It seems though that I will indeed need to use your codes to do the > interpolation/extrapolation mentioned within the section 2.9 of the paper > you sent since my potential curves are still awkward in the angle range > corresponding to the onset regions of the rdf. So that will definitely save > the day also - thanks for sending me that paper. > > Other than that, hopefully IBI will keep working later on, when I move to > the non-bonded in other mappings cherishing more than one bead type, which > will be more challanging since the effect one pair potential has in the > spatial arrangement of other pairs is meant to be more intense in xtalline > solids compared to liquids. > > In any case, thanks a lot once again! It is no scientific prize, but your > name will totally be in the acknowledgements of my thesis!! :D > Celillia, sorry for being late to the party! I am glad you found the problem! And thanks Marvin for helping out here. There is one example in the tutorials about scaling,see: https://github.com/votca/votca/blob/master/csg-tutorials/urea-water/ibi/settings.xml#L52C1-L58 And the VOTCA pdf manual is obsolete, please use our online documentation at https://www.votca.org instead. Christoph > [image: Marvin.png] > > Em domingo, 7 de maio de 2023 às 19:32:10 UTC+2, Marvin Bernhardt escreveu: > >> Hi Cecília, >> >> unfortunately I did not have time to run it myself. But I had a quick >> look at the files and I think I see what is missing to activate post-update >> scaling. It should have "scale" in post_update: >> ``` >> <post_update>scale</post_update> >> <post_update_options> >> <scale>0.25</scale> >> </post_update_options> >> ``` >> Maybe you can try that out, I keep my fingers crossed :) >> >> >> On Saturday, 6 May 2023 at 12:33:43 UTC+2 Cecília Álvares wrote: >> >>> (more pictures lying of distributions in farther steps. >>> *PS:* In the figure that I showed you before the last message you sent, >>> step 30 is a weird distribution whilst in the image below it isnt. This is >>> because I ran the simulation to generate the results shown above with a >>> smaller amount of atoms in order to get it done faster. That's why they >>> dont match. In any case, the problem seems to be there regardless of how >>> big the box is and I do gather enough microstates to do the statistics. >>> >>> These curves here and the one from my message above with steps 5,6 and 7 >>> are from a same simulation containing the same amount of superatoms as in >>> the file I sent you (1500), and with optimization occuring only in the >>> angle, so that maybe it is more comparable with your case. >>> [image: marvin_picture2.png] >>> >>> Em sábado, 6 de maio de 2023 às 12:09:52 UTC+2, Cecília Álvares escreveu: >>> >>>> Also, here comes potential curves and probability distribution curves >>>> that are of consecutive steps as you asked. You can see that indeed it is >>>> going back and forth (at least in these three steps that I prepared). And >>>> despite understanding how the "pre-factor" idea can help with the cause, I >>>> dont think that it will really save the day without implementing your codes >>>> to take care of the onset interpolation. This is because in my case I have >>>> a lot of onset regions with very tiny values which will result in huge >>>> values when boltzmann inverted (specially in the g(r), if I go for >>>> optimizing non-bonded later on, since my material is xrystalline). >>>> >>>> You can see that I have these weird peaks that are artificially created >>>> without the interpolation. I think this is what causing everything to go to >>>> hell. But I havent managed to use the codes you mentioned in that VOTCA >>>> branch to give you a feedback. >>>> >>>> Anyways, thanks a lot for helping me with all of this ! :) >>>> [image: pictures_marvin.png] >>>> >>>> Em sábado, 6 de maio de 2023 às 11:54:57 UTC+2, Cecília Álvares >>>> escreveu: >>>> >>>>> Hey Marvin, >>>>> >>>>> In fact, maybe I am not setting the scaling factor correctly. I had >>>>> seen page 56 of VOTCA's manual and understood the factor to be an option >>>>> <scale> [value you want] </scale> " that should be input inside the >>>>> <post_update_options> (which is inside <inverse>). I mean, it does say in >>>>> page 56 of the manual, "*post_update_options.scale *: scale factor >>>>> for the update (default 1.0)". But now that I took a look comparing the >>>>> results with and without the factor, instead of simply looking at them two >>>>> separately, I realize that the curves are exactly the same. So the factor >>>>> that I am setting is not doing anything.... >>>>> >>>>> Sure, I have no problem sharing the files here. If you want to run, I >>>>> suggest that you try optimizing the bonded potentials (and also only the >>>>> angle, leaving the bond potential constant throughout the IBI) because it >>>>> is simpler than doing it for the g(r). I will put it all here in a zip >>>>> file. Thanks a lot for the offer. >>>>> PS: In fact, after I re-read your previous email, I realized I had >>>>> misread the first sentence of your phrase: in my case, I was much more >>>>> surprised that the optimization of the bonded didnt work. The g(r)s have >>>>> very complicated shapes, so in fact for me it is more shocking not to be >>>>> able to reproduce the angle distribution than the g(r) - at least not >>>>> without the interpolation in the onset regions you mentioned in the paper. >>>>> >>>>> Based on your previous suggestion: yesterday I tried narrowing the min >>>>> and the max to do no accomodate the onset regions and splitting the angles >>>>> into two types, but upon looking at the results quickly, the iterations >>>>> are >>>>> not getting better either, but then I need to analyse this more carefully >>>>> still. >>>>> Em sábado, 6 de maio de 2023 às 10:23:49 UTC+2, Marvin Bernhardt >>>>> escreveu: >>>>> >>>>>> Regarding your last picture: I observe that all the even iterations >>>>>> (10, 30, 100) have spikes at different positions compared to the odd >>>>>> iterations (15, 19). I really would like to see a plot with consecutive >>>>>> iterations, i.e. 30-36 to see if it goes forth and back. However, this >>>>>> should be solved by a scaling factor. Did you try a small scaling factor >>>>>> like 0.1 or smaller? >>>>>> >>>>>> I can offer you to run IBI on my computer and have a closer look. If >>>>>> you don't want to share the files here, you can also send me a direct >>>>>> E-Mail. >>>>>> >>>>>> Cheers >>>>>> >>>>>> On Friday, 5 May 2023 at 11:29:33 UTC+2 Cecília Álvares wrote: >>>>>> >>>>>>> PS: sorry, the y axis says g(r) but it is the angle probability >>>>>>> distribution >>>>>>> >>>>>>> Em sexta-feira, 5 de maio de 2023 às 11:24:45 UTC+2, Cecília Álvares >>>>>>> escreveu: >>>>>>> >>>>>>>> (1) indeed I spotted that in some cases they oscilate back and >>>>>>>> forth around the target distribution (I am attaching a pic as an >>>>>>>> example). >>>>>>>> However, this is not something that putting a factor < 1 was able to >>>>>>>> solve. >>>>>>>> (2) no, I am working in the NVT ensemble. >>>>>>>> (3) my thermostat is working: the temperature is quite well >>>>>>>> equilibrated (no weird spikes). The timestep us also small (I am using >>>>>>>> 5fs >>>>>>>> atm). >>>>>>>> (4) me too :"D >>>>>>>> >>>>>>>> R: Regarding the implementation in Votca: I saw that link in the >>>>>>>> paper. So indeed the interpolation scheme at the onset region that is >>>>>>>> mentioned in the paper is not implemented in the basic VOTCA >>>>>>>> installation >>>>>>>> and we need to use those codes in the branch you mentioned, right? >>>>>>>> >>>>>>>> R: Regarding the bonded potentials: Good idea. That is actually >>>>>>>> something I did not try. I test it. >>>>>>>> >>>>>>>> Photo below: evolution of the angle distribution in a scenario in >>>>>>>> which I am optimizing only one potential (i.e., the angle potential) + >>>>>>>> using a factor of 0.25 >>>>>>>> [image: marvin2.png] >>>>>>>> >>>>>>>> Em sexta-feira, 5 de maio de 2023 às 09:08:04 UTC+2, Marvin >>>>>>>> Bernhardt escreveu: >>>>>>>> >>>>>>>>> Regarding optimizing non-bonded potentials in crystals, just a >>>>>>>>> list of things I would check: >>>>>>>>> Are the distributions at the iterations oscillating around the >>>>>>>>> target distribution? Or is it rather a slow approach that never gets >>>>>>>>> there? >>>>>>>>> Or is it chaotic? >>>>>>>>> Are you working at constant pressure? If so, I would try at >>>>>>>>> constant volume. >>>>>>>>> Is your thermostat working and your time step small enough such >>>>>>>>> that the temperature is always as expected in each iteration? >>>>>>>>> Well possible, that it just does not work for your system, >>>>>>>>> however, I am really surprised, that separating out a single >>>>>>>>> potential in >>>>>>>>> the whole system did not work. >>>>>>>>> >>>>>>>>> Regarding the implementation in Votca: >>>>>>>>> It is still in the branch csg/mulit-iie2 at GitHub, you can build >>>>>>>>> it from there. It has all the methods from the paper. >>>>>>>>> >>>>>>>>> Regarding the bonded potentials: >>>>>>>>> For this situation it helps to restrict the range such that the >>>>>>>>> problematic regions are not included. Votca should then extrapolate >>>>>>>>> bonded >>>>>>>>> potentials linearly. >>>>>>>>> >>>>>>>>> >>>>>>>>> On Thursday, 4 May 2023 at 14:46:49 UTC+2 Cecília Álvares wrote: >>>>>>>>> >>>>>>>>>> Let me just ask one more question if I may: >>>>>>>>>> >>>>>>>>>> In the section 2.9 of your paper, you talk about how the >>>>>>>>>> algorithm is set to create an "alternative RDF" which cherishes an >>>>>>>>>> interpolation in the onset region, where the values of the original >>>>>>>>>> RDF >>>>>>>>>> tend to be very small and the region tend to be poorly sampled >>>>>>>>>> (which is a >>>>>>>>>> quite good idea btw :) ). In the paper it specifically says range of >>>>>>>>>> values >>>>>>>>>> that you guys have had good experience with applying this >>>>>>>>>> interpolation >>>>>>>>>> procedure. In the abstract of the paper it says that the methods are >>>>>>>>>> implemented in VOTCA. Do you mean only the specific numerical >>>>>>>>>> methods you >>>>>>>>>> are using to do the iterative process or do you include also other >>>>>>>>>> specific >>>>>>>>>> things such as the interpolation protocol you described in section >>>>>>>>>> 2.9? >>>>>>>>>> >>>>>>>>>> I am asking because in my case, sometimes, the distribution >>>>>>>>>> coming from the CG simulation ends up having small values that >>>>>>>>>> sometimes >>>>>>>>>> oscillates a bit back and forward in the onset region but the g(r) >>>>>>>>>> has >>>>>>>>>> values a bit larger than the value you mentioned in the paper for >>>>>>>>>> which the >>>>>>>>>> itnerpolation is done (1E-4). This causes weird potentials to happen >>>>>>>>>> which >>>>>>>>>> could be the reason why everything is going to hell. I am attaching a >>>>>>>>>> figure to illustrate the point. Is there a way in which I can change >>>>>>>>>> myself >>>>>>>>>> the value of the threshold for which I want to apply the >>>>>>>>>> interpolation? >>>>>>>>>> Maybe in my case I would need to use values higher than 1E-4. It >>>>>>>>>> could >>>>>>>>>> totally save the day and also make sense: since I am simulating a >>>>>>>>>> xtalline >>>>>>>>>> material whose superatoms are allowed less movement compared to a >>>>>>>>>> liquid, >>>>>>>>>> the setup of my interpolation needs to be more strict for the IBI to >>>>>>>>>> work. >>>>>>>>>> >>>>>>>>>> [image: marvin.png] >>>>>>>>>> >>>>>>>>>> Em quinta-feira, 4 de maio de 2023 às 12:25:09 UTC+2, Cecília >>>>>>>>>> Álvares escreveu: >>>>>>>>>> >>>>>>>>>>> I think at this point I may be ready to just say that indeed IBI >>>>>>>>>>> cannot be used to converge to a potential that is able to reproduce >>>>>>>>>>> the >>>>>>>>>>> structure of xtalline materials (or at least the material I am >>>>>>>>>>> studying). >>>>>>>>>>> >>>>>>>>>>> I've tried >>>>>>>>>>> (1) diminishing the factor used to update the potential (as you >>>>>>>>>>> mentioned) and it did not work. >>>>>>>>>>> (2) updating literally only one potential at a time in the IBI >>>>>>>>>>> and keeping the others literally constant either in the BI >>>>>>>>>>> potential or in >>>>>>>>>>> analytical forms that are able to reproduce perfectly the >>>>>>>>>>> probability >>>>>>>>>>> distributions. This would discard the possibility of dependence on >>>>>>>>>>> the >>>>>>>>>>> degrees of freedom in that sense that the update of one potential is >>>>>>>>>>> affecting the distributions related to other potentials. >>>>>>>>>>> (3) Although the result is not meant to be bin-size-dependent, I >>>>>>>>>>> tried playing with the bin size of both, the references I am >>>>>>>>>>> feeding to >>>>>>>>>>> VOTCA, and of the distributions it is meant to built as the >>>>>>>>>>> iterative >>>>>>>>>>> process runs for the different potentials. I thought maybe I was not >>>>>>>>>>> setting up "proper" bin sizes for the algorithm. >>>>>>>>>>> (4) I tried dividing the angles lying within each of the two >>>>>>>>>>> peaks in the initial figure I showed into two different angle types >>>>>>>>>>> and it >>>>>>>>>>> also did not work. >>>>>>>>>>> (5) I read your paper and tried to be more careful with issues >>>>>>>>>>> that you raised in section 2.9 related to the smoothness of the >>>>>>>>>>> distributions in the onset region (although VOTCA is supposed to >>>>>>>>>>> take care >>>>>>>>>>> of this internally apparently via the extrapolation methodology). >>>>>>>>>>> Although >>>>>>>>>>> section 2.10 bring up issues related to IMC, I also tried some more >>>>>>>>>>> ideas >>>>>>>>>>> that came to mind from reading that section and it didnt work. >>>>>>>>>>> (6) I've tried keeping analytical forms for the bonded >>>>>>>>>>> potentials (I happen to have analytical forms that perfectly >>>>>>>>>>> reproduce the >>>>>>>>>>> distributions) and optimize the non-bonded and it also doesnt work. >>>>>>>>>>> >>>>>>>>>>> Naturaly, in all cases, together with weird distributions, my >>>>>>>>>>> potentials are also going to hell as the iterative procedure goes >>>>>>>>>>> on (which >>>>>>>>>>> explains why the corresponding distributions are weird). >>>>>>>>>>> >>>>>>>>>>> For sure the problem doesnt have to do with the "sharpness" of >>>>>>>>>>> the probability distribution curves (due to the xtalline material >>>>>>>>>>> being >>>>>>>>>>> highly ordered) cause I tried to feed "artificial" target >>>>>>>>>>> distributions >>>>>>>>>>> that are wide and thus less step and I dont converge to anything >>>>>>>>>>> reasonable >>>>>>>>>>> either. >>>>>>>>>>> >>>>>>>>>>> Maybe the shape of the distributions for xtalline materials is >>>>>>>>>>> not friendly to be used within IBI to converge to a potential, >>>>>>>>>>> idk... >>>>>>>>>>> Well.. >>>>>>>>>>> >>>>>>>>>>> Em quarta-feira, 26 de abril de 2023 às 15:19:19 UTC+2, Cecília >>>>>>>>>>> Álvares escreveu: >>>>>>>>>>> >>>>>>>>>>>> (In any case let me try your factor idea, some other stuff that >>>>>>>>>>>> came to mind + finish reading your paper so that maybe I have more >>>>>>>>>>>> useful >>>>>>>>>>>> info on the problem) >>>>>>>>>>>> Em quarta-feira, 26 de abril de 2023 às 14:05:06 UTC+2, Cecília >>>>>>>>>>>> Álvares escreveu: >>>>>>>>>>>> >>>>>>>>>>>>> Indeed, this could be the reason why I have this weird >>>>>>>>>>>>> non-smoothness in the plots I sent in my 2nd message (the ones >>>>>>>>>>>>> concerning a >>>>>>>>>>>>> less coarsened mapping), because indeed in this case I was >>>>>>>>>>>>> optimizing all >>>>>>>>>>>>> the three bonded potentials at once. I will try not doing them at >>>>>>>>>>>>> the same >>>>>>>>>>>>> time and see if the smoothness-issue improves. >>>>>>>>>>>>> >>>>>>>>>>>>> But then this would not explain the issues I had in the >>>>>>>>>>>>> original post I made, which concerned another mapping (a highly >>>>>>>>>>>>> coarsened >>>>>>>>>>>>> one). If the problem was a matter of optimizing more than one >>>>>>>>>>>>> bonded >>>>>>>>>>>>> potential at once, I should have had good results when I tried to >>>>>>>>>>>>> do IBI >>>>>>>>>>>>> only for one angle type and kept the potential for bonds constant >>>>>>>>>>>>> (at a BI >>>>>>>>>>>>> guess) throughout the procedure. But unfortunately my angle >>>>>>>>>>>>> distribution >>>>>>>>>>>>> still converges to something ultra weird with 3 peaks. >>>>>>>>>>>>> >>>>>>>>>>>>> PS: maybe my last message was too big and maybe it was >>>>>>>>>>>>> confusing, but the figures I sent in my 1st message and in my 2nd >>>>>>>>>>>>> message >>>>>>>>>>>>> are for different mappings. In the first one (let's call it >>>>>>>>>>>>> mapping A), I >>>>>>>>>>>>> have only 1 bond type and 1 angle type. For this one I did try >>>>>>>>>>>>> optimizing >>>>>>>>>>>>> separately to see if it would fix the problem and yet I reached >>>>>>>>>>>>> weird >>>>>>>>>>>>> results. The second message had figures of a less coarsened >>>>>>>>>>>>> mapping (let's >>>>>>>>>>>>> call it mapping B) in which I somewhat successfully converge to >>>>>>>>>>>>> potentials >>>>>>>>>>>>> that yield more or less rightful distributions (apart from the >>>>>>>>>>>>> smoothness >>>>>>>>>>>>> issue). I only brought up the results of the second mapping to >>>>>>>>>>>>> show that >>>>>>>>>>>>> the same strategy "worked" for deriving bonded potentials via IBI >>>>>>>>>>>>> for >>>>>>>>>>>>> another mapping. Sorry if I made it more confusing! >>>>>>>>>>>>> >>>>>>>>>>>>> Em quarta-feira, 26 de abril de 2023 às 08:29:58 UTC+2, Marvin >>>>>>>>>>>>> Bernhardt escreveu: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hey Cecília, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Oh ok, then it is probably not the interaction with the >>>>>>>>>>>>>> non-bonded terms, that causes issues. But I believe something >>>>>>>>>>>>>> similar is >>>>>>>>>>>>>> going on, that indeed has something to do with your system being >>>>>>>>>>>>>> a >>>>>>>>>>>>>> solid/crystal: >>>>>>>>>>>>>> IBI is a very good potential update scheme, when the degrees >>>>>>>>>>>>>> of freedom are well separated. For molecules in liquids, angles >>>>>>>>>>>>>> and bonds >>>>>>>>>>>>>> are usually well separated, i.e. changing the potential of one, >>>>>>>>>>>>>> does not >>>>>>>>>>>>>> affect the dist of the other much. But multiple occurrences of >>>>>>>>>>>>>> equivalent >>>>>>>>>>>>>> DoFs also need to be well separated for IBI to work well. In >>>>>>>>>>>>>> your case, >>>>>>>>>>>>>> consider a single angle potential between three beads in the >>>>>>>>>>>>>> crystal is >>>>>>>>>>>>>> changed, but all the others are kept constant. It will change the >>>>>>>>>>>>>> distribution of that angle, but also have effect on different >>>>>>>>>>>>>> angles. In >>>>>>>>>>>>>> that case IBI is not providing a good potential update at each >>>>>>>>>>>>>> iteration. >>>>>>>>>>>>>> What is happening in detail, I believe, is that the angle >>>>>>>>>>>>>> potential of all angles is updated by IBI, but this leads to an >>>>>>>>>>>>>> “overshoot”. The next iteration, IBI tries to compensate, but >>>>>>>>>>>>>> overshoots >>>>>>>>>>>>>> again in the other direction. You can easily test if this is >>>>>>>>>>>>>> what is >>>>>>>>>>>>>> happening, plotting even and uneven iterations separately, i.e. >>>>>>>>>>>>>> compare a >>>>>>>>>>>>>> plot at iterations 10, 12, 14 with 11, 13, 15. >>>>>>>>>>>>>> This has happened to me before with ring molecules, where the >>>>>>>>>>>>>> situation is similar. A possible solution is to scale the >>>>>>>>>>>>>> update, by some >>>>>>>>>>>>>> factor between 0 and 1 (I'd try 0.25). >>>>>>>>>>>>>> >>>>>>>>>>>>>> Also test this for the bond potential, I guess this is >>>>>>>>>>>>>> happening there too, otherwise it should converge within ~20 >>>>>>>>>>>>>> iterations. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Greetings, >>>>>>>>>>>>>> Marvin >>>>>>>>>>>>>> On Tuesday, 25 April 2023 at 10:25:59 UTC+2 Cecília Álvares >>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hey Marvin, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks a lot for the reply! >>>>>>>>>>>>>>> I will have a look on the paper right now and do some >>>>>>>>>>>>>>> thinking. In fact, I wanted to test the possibility of >>>>>>>>>>>>>>> optimizing the >>>>>>>>>>>>>>> bonded potentials first and, after its optimization is done, >>>>>>>>>>>>>>> optimize the >>>>>>>>>>>>>>> non-bonded. So basically there is no optimization of non-bonded >>>>>>>>>>>>>>> whatsover >>>>>>>>>>>>>>> being done in my simulation. To build the target distributions, >>>>>>>>>>>>>>> I sampled >>>>>>>>>>>>>>> an atomistic system in which the non-bonded forces were >>>>>>>>>>>>>>> artificially >>>>>>>>>>>>>>> removed. After having a trajectory file of this AA system, I >>>>>>>>>>>>>>> built the >>>>>>>>>>>>>>> corresponding target distributions to be used in VOTCA with >>>>>>>>>>>>>>> csg_stat. For >>>>>>>>>>>>>>> what is worth it, the target distributions of angle and bond >>>>>>>>>>>>>>> don't seem at >>>>>>>>>>>>>>> all weird relative to the "real ones", of when non-bonded >>>>>>>>>>>>>>> forces exist. And >>>>>>>>>>>>>>> then, after having the target distributions, I set up the CG MD >>>>>>>>>>>>>>> simulations >>>>>>>>>>>>>>> within the IBI to have only bonded potential also. So, besides >>>>>>>>>>>>>>> there being >>>>>>>>>>>>>>> no non-bonded potential optimization, there is also no >>>>>>>>>>>>>>> non-bonded forces at >>>>>>>>>>>>>>> all in my CG system. But I dont think this should be a problem, >>>>>>>>>>>>>>> right? It >>>>>>>>>>>>>>> makes sense to entrust the CG bonded potentials to reproduce >>>>>>>>>>>>>>> the target >>>>>>>>>>>>>>> distributions of the AA bonded potentials. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> What I did try also, and that is in allignment with your >>>>>>>>>>>>>>> idea, was to set up two IBI runs: (1) one run to optimize >>>>>>>>>>>>>>> *only* the potential for the bonds and keep the angle >>>>>>>>>>>>>>> potential active (in this case the latter comes from a simple >>>>>>>>>>>>>>> BI) and (2) >>>>>>>>>>>>>>> one run to optimize only the potential for the angles and keep >>>>>>>>>>>>>>> the bond >>>>>>>>>>>>>>> potential active (in this case the latter comes from a simple >>>>>>>>>>>>>>> BI). In the >>>>>>>>>>>>>>> case (1) it seems that I converge to a potential for bonds that >>>>>>>>>>>>>>> is quite >>>>>>>>>>>>>>> able to reproduce the corresponding distribution, while in the >>>>>>>>>>>>>>> case (2) I >>>>>>>>>>>>>>> converge more and more to potentials that give super weird >>>>>>>>>>>>>>> distributions >>>>>>>>>>>>>>> (like with three weird peaks, as I showed in the figure above) >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Concerning the phase of the system: it is a solid system. >>>>>>>>>>>>>>> More specifically, it is a coarsened grained version of ZIF8 in >>>>>>>>>>>>>>> which the >>>>>>>>>>>>>>> whole repeating unit was assumed to be one bead. I know that >>>>>>>>>>>>>>> IBI has not at >>>>>>>>>>>>>>> all been developed for solids and even further not for MOFs - >>>>>>>>>>>>>>> the goal is >>>>>>>>>>>>>>> actually to derive potentials in the CG level using many >>>>>>>>>>>>>>> different >>>>>>>>>>>>>>> strategies (IBI, FM, relative entropy) and evaluate the >>>>>>>>>>>>>>> results. In any >>>>>>>>>>>>>>> case, I dont think that the fact that my system is a xtalline >>>>>>>>>>>>>>> solid could >>>>>>>>>>>>>>> be the reason why my results are super weird (right?). It seems >>>>>>>>>>>>>>> like such a >>>>>>>>>>>>>>> simple system when in the CG level. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> For what is worth it, I am also assessing different >>>>>>>>>>>>>>> mappings. Following the same strategy of optimizing first >>>>>>>>>>>>>>> bonded-potential >>>>>>>>>>>>>>> for a less coarsened mapping (2 beads), I am able to reach less >>>>>>>>>>>>>>> weird >>>>>>>>>>>>>>> results. For example, you can find below the evolution of the >>>>>>>>>>>>>>> corresponding >>>>>>>>>>>>>>> distributions as I perform more iterations for this system (it >>>>>>>>>>>>>>> has one bond >>>>>>>>>>>>>>> type and two angle types). I think there is still a problem >>>>>>>>>>>>>>> since we can >>>>>>>>>>>>>>> see some tendency of the distributions becoming non-smooth as I >>>>>>>>>>>>>>> do more >>>>>>>>>>>>>>> iterations, but the results are definitely less weird. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [image: picture.png] >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Em segunda-feira, 24 de abril de 2023 às 20:50:14 UTC+2, >>>>>>>>>>>>>>> Marvin Bernhardt escreveu: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Cecília, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I once encountered similar problems with bonded and >>>>>>>>>>>>>>>> non-bonded interactions. See Fig. 9 of this paper >>>>>>>>>>>>>>>> <https://pubs.acs.org/doi/10.1021/acs.jctc.2c00665>. In >>>>>>>>>>>>>>>> short: The problem was that the potential update of the >>>>>>>>>>>>>>>> non-bonded has some >>>>>>>>>>>>>>>> influence on the bonded distribution, and vice versa. But the >>>>>>>>>>>>>>>> potential >>>>>>>>>>>>>>>> update is calculated as if they were independent. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The fix in my case was to update the two interactions >>>>>>>>>>>>>>>> alternately using `<do_potential>1 0</do_potential>` for >>>>>>>>>>>>>>>> bonded and `<do_potential>0 1</do_potential>` for >>>>>>>>>>>>>>>> non-bonded interactions. You could try something similar. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Otherwise, is your system liquid? Are there non-bonded >>>>>>>>>>>>>>>> interactions that you are optimizing at the same time? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Greetings, >>>>>>>>>>>>>>>> Marvin >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Monday, 24 April 2023 at 16:56:42 UTC+2 Cecília Álvares >>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hey there, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I am currently trying to derive bonded potentials of a >>>>>>>>>>>>>>>>> very simple CG system (containing only one bond type and one >>>>>>>>>>>>>>>>> angle type) >>>>>>>>>>>>>>>>> using IBI. However, I have been failing miserably at doing >>>>>>>>>>>>>>>>> it: instead of >>>>>>>>>>>>>>>>> reaching potentials that are better and better at reproducing >>>>>>>>>>>>>>>>> the target >>>>>>>>>>>>>>>>> distributions for the bond and for the angle, I end up having >>>>>>>>>>>>>>>>> weider and >>>>>>>>>>>>>>>>> weider distributions as I do the iterations. I am posting a >>>>>>>>>>>>>>>>> plot of the >>>>>>>>>>>>>>>>> bond and angle distributions to give a glimpse on the >>>>>>>>>>>>>>>>> "weirdness". I have >>>>>>>>>>>>>>>>> already tried: >>>>>>>>>>>>>>>>> (1) providing very refined (small bin size and a lot of >>>>>>>>>>>>>>>>> bins) target distributions of excelent quality (meaning not >>>>>>>>>>>>>>>>> noisy at all) >>>>>>>>>>>>>>>>> for the bond and the angle. Similarly, I have also tried >>>>>>>>>>>>>>>>> using less refined >>>>>>>>>>>>>>>>> target distributions (larger bin sizes and less amount of >>>>>>>>>>>>>>>>> bins). >>>>>>>>>>>>>>>>> (2) varied a lot the setup in the settings.xml concerning >>>>>>>>>>>>>>>>> bin sizes for the distributions to be built at each iteration >>>>>>>>>>>>>>>>> from the >>>>>>>>>>>>>>>>> trajectory file. I have tried very small bin sizes as well as >>>>>>>>>>>>>>>>> large bin >>>>>>>>>>>>>>>>> sizes. >>>>>>>>>>>>>>>>> (3) increasing the size of my simulation box hoping that >>>>>>>>>>>>>>>>> maybe it was all a problem of not having "enough statistics" >>>>>>>>>>>>>>>>> to build good >>>>>>>>>>>>>>>>> distributions at each iteration within the trajectory file I >>>>>>>>>>>>>>>>> was collecting >>>>>>>>>>>>>>>>> from my simulations. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> None of these things has worked and I think I ran out of >>>>>>>>>>>>>>>>> ideas of what could possibly be the cause of the problem. >>>>>>>>>>>>>>>>> Does anyone have >>>>>>>>>>>>>>>>> any insights? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I am also attaching my target distributions (this is the >>>>>>>>>>>>>>>>> scenario in which I am feeding target distributions lot of >>>>>>>>>>>>>>>>> points and >>>>>>>>>>>>>>>>> smaller bin size) and the settings.xml file for what is worth >>>>>>>>>>>>>>>>> it. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: plots.png] >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/220aeac6-1ae0-4ad7-ae1e-6124aa435469n%40googlegroups.com > <https://groups.google.com/d/msgid/votca/220aeac6-1ae0-4ad7-ae1e-6124aa435469n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e4kNKS_xdNcX7JDTiEm0JtHN1uKpm82yZwb812-XEMM7Q%40mail.gmail.com.
