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]. 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.
