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/66d35a14-bbb4-416c-8f53-29546ba375bdn%40googlegroups.com.
