Hello Cecilia, Thank you for the info. It is very helpful indeed.
On Sunday, June 18, 2023 at 12:56:55 PM UTC-4 Cecília Álvares wrote: > Hello Sanjeet, > > So, in the end of the day, I, myself, ended up using IBI only for the > non-bonded. I am using a simple BI to derive the bonded potentials. > > I never explored this rerun command to remove non-bonded forces. I am also > skepitcal on how this would work (although I never read much about it). > When I was with that plan of optimizing bonded first in head, I ran a > simulation in the AA level without the non-bonded force-fields (so only > with bonded), saved a bunch of microstates of the equilibrated system, and > derived the reference bond and angle distributions for the CG > representation from these saved AA microstates. *Note that this may not > work for all the systems universely*: sometimes the resulting reference > CG structure you get from simulating the AA only with bonded forces is very > "irrealistic" when compared with the actual, rightful structure your system > should have in the corresponding CG level (i.e., the one corresponding to > when you simulate the AA with both bonded and non-bonded). For example, > angle distributions in the CG level that should have 2 peaks when > simulating the AA with the complete set of force-fields may turn out to > have only one peak (as if the two peaks merged) in the AA simulated only > with bonded force fields. So if you see that the structural results you get > from running the AA simulation only with bonded force-fields are very > unrealistic compared to the rightful structure your system should have, I > would not recommend doing the optimization of the CG bonded potentials > using those structural results of AA sampled with bonded contributions > only. It is better to use as reference the structural results of the AA > system simulated with bonded and non-bonded. > > Em domingo, 18 de junho de 2023 às 02:35:08 UTC+2, Sanjeet Singh escreveu: > >> 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/440f5c33-efce-4ac7-8e90-4df9192b5cb7n%40googlegroups.com.
