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 (not optmizing/altering at all any other bonded potential). 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, which I even 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/908a5f97-91cb-48df-935f-c649c22912b3n%40googlegroups.com.
