2016-10-27 7:12 GMT-06:00 Gustavo Rondina <rond...@gmail.com>: > Hello VOTCA folks, > > Since LAMMPS dump files provide no topological information, I'm doing as > instructed in the manual and using a XML topology. However, I'm not quite > sure how to specify more than one bond of a single type. > > To simplify my question, suppose I have a bead-spring polymer model with 8 > beads per chain (this would be the reference system). My topology XML file > looks like this in this case: > > <topology name="traj.dump"> > <molecules> > <clear/> > <molecule name="CHAIN" nmols="1000" nbeads="8"> > <bead name="A1" type="1" mass="1.0." q="0.0"/> > <bead name="A2" type="1" mass="1.0." q="0.0"/> > <bead name="A3" type="1" mass="1.0." q="0.0"/> > <bead name="A4" type="1" mass="1.0." q="0.0"/> > <bead name="A5" type="1" mass="1.0." q="0.0"/> > <bead name="A6" type="1" mass="1.0." q="0.0"/> > <bead name="A7" type="1" mass="1.0." q="0.0"/> > <bead name="A8" type="1" mass="1.0." q="0.0"/> > </molecule> > </molecules> > <bonded> > <bond><name>bond</name><beads>CHAIN:A1 CHAIN:A2</beads></bond> > <bond><name>bond</name><beads>CHAIN:A2 CHAIN:A3</beads></bond> > <bond><name>bond</name><beads>CHAIN:A3 CHAIN:A4</beads></bond> > <bond><name>bond</name><beads>CHAIN:A4 CHAIN:A5</beads></bond> > <bond><name>bond</name><beads>CHAIN:A5 CHAIN:A6</beads></bond> > <bond><name>bond</name><beads>CHAIN:A6 CHAIN:A7</beads></bond> > <bond><name>bond</name><beads>CHAIN:A7 CHAIN:A8</beads></bond> > </bonded> > </topology> > > There is a single bond type in the system, i.e., the bonds A1-A2, A2-A3, > ..., A7-A8, are all of the same type. I've tried to list them in a single > <bond> block, however it didn't allow me to do that. What seems to work is > the setup shown above, where multiple <bond> blocks all have the same name. > > My intention is to tell that all these bonds are of the same type. Does this > setup work as intended? As I said, it seems to work, but I don't know > whether I'm doing it in the proper way of if it's only working by accident. Jakub, please correct me if I am wrong, but I think the xml topology will just setup the bond. And remember you only need to tell VOTCA that there are bonds in the topology if you want to analyze them or if you need the exclusions. LAMMPS won't know about the information in the xml topology file. To analyze them (using e.g. csg_stat) you will still need to do a 1:1 mapping xml file listing all the bonds you want to average over.
Christoph > > My VOTCA version is 1.4_rc1. > > Cheers, > Gustavo > > > -- > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
