Thanks, I set the <min> value as 3.5A following your suggestion, now it seems to go well and the weird step-shaped pair potential has been disappeared.
在 2018年12月9日星期日 UTC+8下午9:25:39，Christoph Junghans写道： > > On Sun, Dec 9, 2018 at 3:13 AM Thomas Meng <[email protected] > <javascript:>> wrote: > > > > Hi, Christoph. Sorry to bother again! > > > > At around the 45th IBI iteration using LAMMPS as the sampling program, I > came across a problem saying that "bond atoms are missing". Then I checked > the pair potential I generated, it looks weird and there comes a strange > 'step-shaped' turn at around 3~4 Angstrom. Noticed that the position is > near where the target RDF becomes non-zero, so I wonder why my system > didn't generate a zero RDF before that point. > > > > Maybe the problem is due to the accumulative effect of the potential > before it? You know, because U_(n+1) = U_(n) + delta_U, so the delta_U > before3~4 Angstrom is always positive in my case and resulted in that > problem? What should I do to solve it? > > That usually means something went wrong with the extrapolation on the > min side, most likely it wasn't steep enough to prevent particles from > coming too close. You will have to play a bit with the r_min for that > interaction. Set it so that the rdf is not quite 0 yet, but so that it > is very steep. As the average steepness is what determines the > extrapolation. > > Christoph > > > > 在 2018年12月8日星期六 UTC+8下午9:21:53，Christoph Junghans写道： > >> > >> On Sat, Dec 8, 2018 at 1:05 AM Thomas Meng <[email protected]> > wrote: > >> > > >> > Thanks, I think I understood what you said about the topol.xml's > bonded definition thing. In order to perform the ibi > >> > calculation, it seems that I need to write a new topol.xml for my > coarse-grained system. Besides, I could also use > >> > a lammps data file as a topol file as you mentioned before with a > little modification to the setting.xml file. However, the > >> > use of lammps data as a topol may not be appropriate for ibi > calculation. > >> > > >> > I tested my polyether system using both the CG configuration' data > and a house-written topol.xml as the topol file to > >> > realize the ibi procedure.Then I compared the resulted RDF generated > by these calculations after only one iteration, > >> > and they are just different (I attached the figures). It could be > obviously observed that the peak of RDF is a bit higher > >> > than the target one, however that is very similiar to the RDF without > considering those bond interactions which I calculated > >> > before. So, I guess that as a topo file, the LAMMPS data didn't > consider the bonded interaction correctly. > >> Yes, I think you are correct, in the RDF from the data files no > >> exclusions seemed to generated, "csg_dump --excl" should confirm that > >> as well. > >> So I guess we still need to improve on the data reader a bit. > >> > >> Christoph > >> > > >> > 在 2018年12月7日星期五 UTC+8下午8:49:08，Christoph Junghans写道： > >> >> > >> >> On Thu, Dec 6, 2018 at 7:29 PM <[email protected]> wrote: > >> >> > > >> >> > 在 2018年12月7日星期五 UTC+8上午6:07:29，Christoph Junghans写道： > >> >> >> > >> >> >> On Thu, Dec 6, 2018 at 9:29 AM <[email protected]> wrote: > >> >> >> > > >> >> >> > Hi, > >> >> >> > > >> >> >> > I'm using VOTCA to coarse-grain a relatively simple polyether > system, [C-C-O-C-C]n, and a super atom just represents a single monomer. > After performing an all-atom simulation in LAMMPS, I got a trajectory file > (trj_tail20.dump) and a final data file (nvt_300K_final.data). I wrote my > own map and topol .xml files, and then use them to calculate the RDF of the > system. > >> >> >> > > >> >> >> > What got me frustrated is that, the RDF I obtained using > csg_stat (figure AA.png) seems to be questionable. Because if I use LAMMPS > to generate the RDF of the central O atom using the final data file, I got > a different result (AA-LAMMPS.png). And the most strange thing is that if I > use OVITO to analyze the CG configuration I converted using the csg_map > command, I got a similar result compared to that of lammps simulation > (AA-OVITO.png). > >> >> >> > > >> >> >> > Because the RDF is a quite important intermediate process file, > so I wonder what resulted in the above difference? And could I trust the > one generated through VOTCA? > >> >> >> > >> >> >> csg_stat has been tested over years, so I don't think there is a > >> >> >> problem in the code. > >> >> >> But I saw your topol.xml has a <bond> section, which in VOTCA > >> >> >> generates a bunch of RDF exclusions, i.e. pairs in a bond aren't > >> >> >> considered for the RDF calculation. You can see that running: > >> >> >> $ csg_dump --top topol.xml --excl > >> >> >> > >> >> >> So if you don't want that just delete that section. > >> >> >> > >> >> > Yes, I've just tested it, the difference surely comes from the > bond definition. However, it's not the > >> >> > bond info in the topol.xml file, but the </cg_bonded> section in > the mapping 'cg.xml' file. If I just > >> >> > delete that section, then I will get the same RDF as the one > generated from LAMMPS (I attached > >> >> > the figure). > >> >> You are right, it is the <cg_bonded> block as you are using a > mapping > >> >> file, which then sets up bonds (with exclusions) in the mapped > system. > >> >> > >> >> However, on a second thought, I don't think the bonds should be > >> >> included in RDF unless you are planning to use the non-bonded > >> >> interactions also between cg beads in the same molecule. > >> >> > >> >> > > >> >> > Thanks. And now I will think about which one is suitable for my > case. > >> >> > > >> >> >> Also in the development version of VOTCA you can use LAMMPS' data > >> >> >> files as topology input directly. > >> >> >> > >> >> > But if I use the LAMMPS data as a top file, then there will be > many unkown molecule problems (it > >> >> > may comes from LAMMPS use numbers to represent atoms and > molecules), so I would rather write > >> >> > a topol.xml myself. However, from my previous test, a data could > be used as a trjactory file, though > >> >> > it only contains one frame, may generate a rough RDF curve. > >> >> Please open an issue on github for each of the "unkown molecule > >> >> problems", maybe we can help fix the code or your input file. > >> >> > >> >> Christoph > >> >> > > >> >> > Anyway, thank you very much for your reply. :) > >> >> > > >> >> > Meng > >> >> > > >> >> >> Christoph > >> >> >> > >> >> >> > > >> >> >> > Meng > >> >> >> > > >> >> >> > P.S. > >> >> >> > The command I used to generate RDF is "csg_stat --top topol.xml > --trj trj.dump --cg cg.xml --options settings.xml" > >> >> >> > > >> >> >> > -- > >> >> >> > 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] <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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