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/81498da5-939b-4105-8eb9-69295bd80555n%40googlegroups.com.
