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. 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] > <javascript:>> 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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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