2017-04-18 10:37 GMT-05:00 <torsten.sac...@gmail.com>: > Hi Denis, > > thanks for the offer and the quick reply! I decided it'd be easiest to alter > the xml topology reader in such a way as to be able to explicitly specify > the residue for each bead as a new but optional keyword "resid" (counting > starts at 1) and thereby completely circumventing the gro-file for building > the topology. This has the merit of allowing one to specify masses and > charges as well. The attached diff introduces that functionality with the > restriction that the resid has to increase monotonically in steps of 1. If > no resid is given, the original functionality is restored. Could this be > included in VOTCA-CTP? Thanks for the patch, here you go: <https://github.com/votca/csg/pull/207> Let's see what Jakub thinks about your change! (For next time: <https://github.com/votca/csg/wiki/BugFix#for-users-contribute-a-bug-fix>)
>>> thanks for your help. It would have been great to have this mentioned >>> somewhere in the manual (at least I cannot seem to be able to find it, my >>> apologies if it is there). However, it does not seem to work in my case. The xmltogology is described in the csg manual: <doc.votca.org/manual.pdf> but not the ctp manual I guess. Thanks and cheers, Christoph > > Best, > Torsten > > On Tuesday, April 18, 2017 at 4:18:58 PM UTC+2, Denis Andrienko wrote: >> >> Hi Torsten, >> >> There are two options: >> >> 1. You can implement the ctp_map without the gromacs reader. >> It is not difficult but we do not have manpower to do this. If you want >> to do this we can help you with coding. You can also visit Mainz and do it >> here. >> >> 2. Generate a fake force-field and topology using GROMACS tools. This is >> what we do at the moment. Not the best solution but it works. ;) If you need >> help with this - do let me know. >> >> Best, >> Denis >> >> On Tue, Apr 18, 2017 at 1:44 PM, <torsten...@gmail.com> wrote: >>> >>> Hi, >>> >>> thanks for your help. It would have been great to have this mentioned >>> somewhere in the manual (at least I cannot seem to be able to find it, my >>> apologies if it is there). However, it does not seem to work in my case. >>> >>> After checking the source and the output of ctp_dump, I think I found the >>> problem. In my case, I have more than one bead per molecule and more than >>> one type of molecules. If I reduce the system to contain just one bead per >>> molecule or just one type of molecules, everything works out. But if I use >>> an example topol.xml file like this: >>> >>>> <topology base="system.gro"> >>>> <molecules> >>>> <clear/> >>>> <define name="UMA" first="1" nbeads="2" nmols="2"/> >>>> <define name="UMB" first="3" nbeads="2" nmols="2"/> >>>> </molecules> >>>> </topology> >>> >>> >>> with an example gro file like this: >>> >>>> Quadrumer >>>> 8 >>>> 1UMA C1 1 -1.103 -0.231 0.214 >>>> 1UMA H1 2 -1.459 -0.073 0.191 >>>> 2UMA C1 3 0.568 0.139 -0.384 >>>> 2UMA H1 4 0.592 0.522 -0.455 >>>> 3UMB C2 5 -0.294 -0.081 -0.227 >>>> 3UMB H2 6 -0.314 -0.466 -0.291 >>>> 4UMB C2 7 0.886 -0.218 0.341 >>>> 4UMB H2 8 0.862 -0.601 0.410 >>>> 1.00000 1.00000 1.00000 >>> >>> >>> beads, residues and molecules are not correctly associated, as can be >>> seen here (something clearly went wrong in case of the third molecule): >>> >>>> [...] >>>> >>>> List of molecules: >>>> molecule: 1 UMA beads: 2 >>>> 0 Name 1:UMA:C1 Type C1 Mass 1 Resnr 0 Resname UMA >>>> 1 Name 1:UMA:H1 Type H1 Mass 1 Resnr 0 Resname UMA >>>> molecule: 2 UMA beads: 2 >>>> 2 Name 1:UMA:C1 Type C1 Mass 1 Resnr 1 Resname UMA >>>> 3 Name 1:UMA:H1 Type H1 Mass 1 Resnr 1 Resname UMA >>>> molecule: 3 UMB beads: 2 >>>> 2 Name 1:UMA:C1 Type C1 Mass 1 Resnr 1 Resname UMA >>>> 3 Name 1:UMA:H1 Type H1 Mass 1 Resnr 1 Resname UMA >>>> molecule: 4 UMB beads: 2 >>>> 4 Name 1:UMB:C2 Type C2 Mass 1 Resnr 2 Resname UMB >>>> 5 Name 1:UMB:H2 Type H2 Mass 1 Resnr 2 Resname UMB >>> >>> >>> If I instead declare all the beads explicitly in the topol.xml file, the >>> programme erroneously creates one residue per bead with no way (that I >>> found) to explicitly state the residue to which the bead belongs. If the >>> system then contains more than one type of molecules, instead of associating >>> 3UMB with the residue number 2, it is assigned number 4. >>> >>> I greatly appreciate any further help you can provide. >>> >>> Best, >>> Torsten >>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "votca-ctp" group. >>> To unsubscribe from this group and stop receiving emails from it, send an >>> email to votca-ctp+...@googlegroups.com. >>> To post to this group, send email to votc...@googlegroups.com. >>> Visit this group at https://groups.google.com/group/votca-ctp. >>> For more options, visit https://groups.google.com/d/optout. >> >> > -- > You received this message because you are subscribed to the Google Groups > "votca-ctp" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca-ctp+unsubscr...@googlegroups.com. > To post to this group, send email to votca-...@googlegroups.com. > Visit this group at https://groups.google.com/group/votca-ctp. > 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.
