On Tue, Oct 16, 2018 at 12:57 AM changseo park <[email protected]> wrote: > > After getting sum advice and searching several queries, I did IBI for > non-bonded, but still I couldn't get the converged non bonded potential > > My system composed of one 30m PNIPAM chain in dilute water. the polymer chain > composed of 3 bead per monomer so total 90 beads. > > Since the PNIPAM has hydrophilic and hydrophobic part, the conformation of > polymer chain is changing, extended to collapsed. So the rdf has broad and > insignificant peak. > > I got the rdf from NPT 300ns atomistic simulation as target and the IBI > process continues in NVT with sd for 10ns per iteration. > > I used post update option smooth (with iteration 3) and scale (0.1) and I > also used do_potential options > > for bonded potential, I used the results of Boltzmann inversion potential. > > the attached file shows the target and new rdf for the system at step_11 and > step_30 > > I'm following the method almost same as this paper with different materials > <J. Phys. Chem. B 2018, 122, 1516−1524> > > the convergence of nonbonded interaction is quite good for this system, > single PAM in water. > > The cause for divergence is, I guess, the quality of RDF. > > I wonder the convergence problem could be solved with better RDF, by doing > another 5set of atomistic simulation with 300ns and getting the rdf from > average value
I don't think that will help, coarse-graining for a system with different phases, like PNIPAM with open and collapsed, is just hard. You might need to develop different coarse-grained potential for each phase. Christoph > > Thanks in advance > > > > > 2018년 10월 6일 토요일 오전 1시 39분 53초 UTC+9, Christoph Junghans 님의 말: >> >> On Fri, Oct 5, 2018 at 7:11 AM changseo park <[email protected]> wrote: >> > >> > >> > Thanks for quick answer!! >> > >> > Okay, the main criteria for convergence is to compare the distribution >> > function one by one with target function >> > >> > In my case, the Convergence sum is start from 15000 and after step 2, it >> > varies from 3000~5000 in every step until more than 300 step >> > >> > when I compared the distribution function, the votca fits the specific >> > peak on the target and switch the specific peaks to others again and >> > again. is it normal process for votca? >> >> I am not 100% sure what you mean but it sounds to me like the IBI is >> overshooting, so you should try to scale the update with the postupd >> scale option. >> > >> > and, The peak location is similar but the y-value has absolute difference >> > comparing to the target, is it OK?? >> > >> > >> > In addtion, I wonder the votca has the potential fixed options which means >> > that, >> > >> > Q. If the A-A rdf shows good convergence comparing to the target >> > distribution, then can I fix the A-A non bonded CG parameter and continue >> > the iteration for other non bonded interaction? (A-B, A-C ...etc)?? >> There is no automatic way to do that. >> >> > >> > Since the iteration could be faster when we start from simple >> > parameterization to complicated parameterization, is there any tips or >> > advice for non bonded IBI instead of iteration for 6 nonbonded parameter >> > at the same time. >> > (for example, <do_potential> options etc....> >> Yeah, you can update one potential per iteration step, using >> do_potential "1 0 0 0 0 0" for the 1st potential and "0 1 0 0 0 0" for >> the 2nd potential and so on. >> >> Christoph >> > >> > Anyway, I really thank to develop votca^^ >> > >> > >> > 2018년 10월 5일 금요일 오후 9시 17분 24초 UTC+9, Christoph Junghans 님의 말: >> >> >> >> On Fri, Oct 5, 2018 at 6:12 AM changseo park <[email protected]> wrote: >> >> > >> >> > TO. VOTCA users >> >> > >> >> > Hi, I'm new user for VOTCA. >> >> > >> >> > I'm researching about one single chain polymer conformation change in >> >> > water dilute system. >> >> > >> >> > I figured out all the errors based on queries on VOTCA and I started >> >> > the IBI step. >> >> > >> >> > For get CG non bonded parameter, I got the bonded interaction from the >> >> > csg_boltzmann and converted to the table form. >> >> > >> >> > There is no problem to do iteration for non-bonded interaction >> >> > >> >> > However, the convergence sum is quite big for iteration. >> >> > >> >> > My convergence criteria is 0.5, but the usual convergence sum is about >> >> > 2000~3000. >> >> The convergence value depends on a lot of things, e.g. # of >> >> interactions, normalization etc., I would put too much belief in that >> >> one number, just look at the RDFs in comparison to the targets and see >> >> if they have converged. >> >> >> >> Christoph >> >> > >> >> > The attached files is about IBI for 6 RDF, non bonded interaction (AA, >> >> > AB, AC, BC, BB, CC) >> >> > >> >> > Plz give me advice to converge non bonded interaction >> >> > >> >> > Thanks in advance >> >> > >> >> > -- >> >> > 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 post to this group, send email to [email protected]. >> >> > Visit this group at https://groups.google.com/group/votca. >> >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> >> >> >> >> -- >> >> Christoph Junghans >> >> Web: http://www.compphys.de >> > >> > -- >> > 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 post to this group, send email to [email protected]. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > 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 post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
