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] <javascript:>> 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).
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. 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] <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. 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.
