Hello Cecilia, I am trying to follow your procedure of optimizing the bonded potential first. I am also using LAMMPS for running all my atomistic simulations.
I am bit confused with removing the non-bonded forces artificially. Are you initially running your simulations with all the interactions (bonded + nonbonded) present in the system, and then using rerun command to artificially remove the non-bonded forces from your system and create a trajectory with only the bonded forces. Greetings, Sanjeet On Tuesday, April 25, 2023 at 4:25:59 AM UTC-4 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/6432e018-d434-4f1c-827d-e840bff7c6c0n%40googlegroups.com.
