On Wed, Nov 28, 2018 at 7:27 PM changseo park <[email protected]> wrote: > > I did IBI for non bond interaction on PNIPAM chain in water. > > I got some reasonable and converged results from iteration. > > There two candidates for convergence > > the red peak shows the rdf from atomistic simulation, and the green shows the > CG parameter candidates. > > step_127 results shows the similarity in absolute value and trend for all non > bond parameter except on absolute value of A-A rdf which shows 1st peak is > much large than 2nd peak > > step_128 shows the similar trend with the reference data, but the absolute > value is lower than the reference value comparing to step_127 data. > > which one could be more acceptable and what's the criteria?? It really depends what you want to do with the model later and if reproducing the first & the second or the first solvation shell only is more important in your case.
Christoph > > Thanks in advance > > 2018년 10월 18일 목요일 오전 12시 18분 24초 UTC+9, Christoph Junghans 님의 말: >> >> On Wed, Oct 17, 2018 at 7:18 AM changseo park <[email protected]> wrote: >> > >> > I already contact with the author you mentioned. Thanks. >> > >> > For checking the dependency of non-bonded potential each other for any >> > system, >> > >> > If I changed the AA potential and the other non bonded rdf is consistent, >> > is it enough to say AA potential is independent to other potential? >> > >> > or still AA non bonded potential could be dependent on other non bonded >> > potential although the other rdf is consistent? >> > >> > How to check and validate that one non-bonded potential is independent on >> > others? >> This is hard question and I don't know of a way to test that >> definitely, but I would say potentials are usually NOT independent, >> but maybe you are luck for your system. >> >> > >> > Thanks in advance. >> > >> > 2018년 10월 17일 수요일 오후 10시 3분 30초 UTC+9, Christoph Junghans 님의 말: >> >> >> >> On Wed, Oct 17, 2018 at 6:41 AM changseo park <[email protected]> wrote: >> >> > >> >> > OK, the more RDF and averaging them will not help. >> >> > >> >> > About my system, PNIPAM in water, I'm working on CG parameterization >> >> > for 280K state which is Coil state based on All atom results( LOPLS + >> >> > TIP4P/2005) >> >> > >> >> > I confirmed that the all atom scale PNIPAM has extended structure at >> >> > 280K and collapsed structure at 320K statistically (300ns trajectory >> >> > and check the histogram of Rg). >> >> > >> >> > And I need the CG parameter only below the LCST(280K). >> >> > >> >> > >> >> > For non bonded parameter, can I converge the non-bonded parameter one >> >> > by one?? >> >> > >> >> > In my system there are 3 bead and total 6 non bonded interaction. >> >> > >> >> > As trial, I tested only A-A non bonded interaction for IBI and I could >> >> > get the potential fully describe the A-A rdf while the IBI for total 6 >> >> > non bonded convergence I couldn't. Can I use this as AA non bonded >> >> > potential?? >> >> > >> >> > I think the potential AA BB CC AB BC AC should be independent? Correct? >> >> > >> >> > Although AB BC AC is dependent on AA BB CC, I think AA BB CC potential >> >> > should be independent >> >> > >> >> > actually, I saw the query that the nonbonded interaction is dependent, >> >> > but there was no exact explanation >> >> > >> >> > Plz attach reference or explain precisely about the reason. >> >> All your questions are very system specific and not really related to >> >> VOTCA itself, so sorry I am not the expert for PNIPAM nor am I a >> >> personal tutor, you will have to figure these answers out by yourself. >> >> If you need more information about coarse-graining of PNIPAM I would >> >> advise you to contact the authors of J. Phys. Chem. B 2018, 122, >> >> 1516−1524. >> >> >> >> Christoph >> >> > >> >> > Always thanks to answer my question. >> >> > >> >> > >> >> > >> >> > 2018년 10월 17일 수요일 오전 2시 4분 35초 UTC+9, Christoph Junghans 님의 말: >> >> >> >> >> >> 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. >> >> >> >> >> >> >> >> -- >> >> 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. 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