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.
