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. Also in the development version of VOTCA you can use LAMMPS' data files as topology input directly. 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.
