2016-07-14 9:44 GMT-06:00 Sikandar Mashayak <[email protected]>: > Hi, > > I tried the pull request code. Below is the topol.xml. Though csg_dump now > dumps correct resname and bead types, the number of beads it counts is more > than it should be. For, the 3-site spce water with 2180 molecules, it prints > > I have 13080 beads in 2180 molecules > > > Whereas it should be 6540 beads in 2180 molecules. I have attached the > output of csg_dump, topol.xml, and spce.dump file that I use. Thanks to Sikandar and Jakub for testing, the new xml topology reader is now part of votca! That should make setup using just an xml file much easier.
Christoph > > Thanks, > Sikandar > > > <topology base="spce.dump"> > <molecules> > <clear/> > <molecule name="SOL" nmols="2180" nbeads="3"> > <bead name="OW" type="OW" mass="16." q="-0.8" /> > <bead name="HW1" type="HW" mass="1." q="0.4" /> > <bead name="HW2" type="HW" mass="1." q="0.4" /> > </molecule> > </molecules> > </topology> > > > > On Thu, Jul 14, 2016 at 8:42 AM, Christoph Junghans <[email protected]> > wrote: >> >> 2016-07-13 23:03 GMT-06:00 Jakub Krajniak <[email protected]>: >> > 2016-07-14 3:52 GMT+02:00 Sikandar Mashayak <[email protected]>: >> >> >> >> Hi, >> >> >> >> I am testing a case in which I want to compute water-water RDF from the >> >> lammps trajectory. >> >> >> >> So, I need to provide xml topology, xml mapping, base *.dump, and >> >> trajectory dump files. However, it is not clear how to specify residue >> >> and >> >> atom name in the mapping file. >> >> >> >> (...) >> >> >> >> Is there a way to specify resname and atom name in topology xml file? >> > >> > >> > AFAIK it's not possible to set resname directly in the xml file. The >> > workaround is to use .gro/pdb or .tpr >> > file as a base topology. But the atom name could be renamed by <rename/> >> > tag. >> Jakub is right, there is no easy way to rename residue nor to rename >> the bead itself ("no" part in id string). >> Even though it wouldn't be hard to implement the latter and rename the >> beads, I think using >> <https://github.com/votca/csg/pull/176> might the better option. >> Have a go, if it works for you, I will merge it. >> >> Christoph >> >> > >> > Best, >> > Jakub >> > >> > -- >> > 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. > > > -- > 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.
