2015-03-13 3:21 GMT-06:00 Daniel Allen <[email protected]>: > Hi Christoph, > > I only start from 0 because VOTCA indexes from 0 doesn't it? If I run > csg_dump --top topol.xml I get: > > "List of molecules: > molecule: 1 PEO16-PBO22 beads: 401 > 0 Name 1::H0 Type H0 Mass 1 Resnr 0 Resname > 1 Name 1::O1 Type O1 Mass 1 Resnr 0 Resname > 2 Name 1::C1 Type C1 Mass 1 Resnr 0 Resname > 3 Name 1::H1 Type H1 Mass 1 Resnr 0 Resname > ..................... > " > > So if I were to specify first=1 then I wouldn't be able to correctly map my > molecules because I would miss the first atom. No, the first number here is the bead id, which starts from 0 (due to the way how c++ counts) and remember csg_dump is a more a debug tool. However, for input file, we are using the human counting system (starting with 1).
Christoph > > Please correct me if I am wrong. > > Cheers, Dan. > > On Tuesday, 10 March 2015 21:08:36 UTC, Christoph Junghans wrote: >> >> 2015-03-10 4:28 GMT-06:00 Daniel Allen <[email protected]>: >> > Thanks for this Christoph, I appreciate it. >> Actually, I found another issue, first <1 is against the spec >> described in the manual. >> I fixed that, too and added a warning: >> >> https://code.google.com/p/votca/source/detail?r=17177c3d1dea8e1b831efa5fdb1f6a16541a2774&repo=csg# >> >> Christoph >> >> > >> > Dan. >> > >> > On Monday, 9 March 2015 23:37:01 UTC, Christoph Junghans wrote: >> >> >> >> 2015-03-09 11:26 GMT-06:00 Daniel Allen <[email protected]>: >> >> > Hi Christoph, >> >> > >> >> > sorry but I am unable to send the file to that email on my gmail so I >> >> > have >> >> > attached it here, I hope that's okay. >> >> I found the bug and fixed it: >> >> >> >> >> >> <https://code.google.com/p/votca/source/detail?r=399952ee16077cb44ea742645f7ac3a759900c1a&name=stable&repo=csg#> >> >> >> >> Christoph >> >> > >> >> > Cheers, Dan. >> >> > >> >> > >> >> > >> >> > On Monday, 9 March 2015 17:00:59 UTC, Christoph Junghans wrote: >> >> >> >> >> >> 2015-03-09 9:26 GMT-06:00 Daniel Allen <[email protected]>: >> >> >> > Hi Votca users, >> >> >> > >> >> >> > I am having trouble setting up my mapping for a system with 2 >> >> >> > different >> >> >> > molecule types. I am using a pdb file containing the all of the >> >> >> > atoms >> >> >> > of >> >> >> > my >> >> >> > polymer and then also the CG water beads that I will be using >> >> >> > (which >> >> >> > I >> >> >> > have >> >> >> > already clustered so there is just a 1:1 mapping for those). >> >> >> > >> >> >> > My topol.xml file looks like this: >> >> >> > >> >> >> > <topology base= "PEO16-PBO22-FULL.pdb"> >> >> >> > <molecules> >> >> >> > <clear/> >> >> >> > <define name="PEO16-PBO22" first="0" nbeads="401" >> >> >> > nmols="128"/> >> >> >> > <define name="WAT" first="51328" nbeads="1" nmols="6667"/> >> >> >> > </molecules> >> >> >> > </topology> >> >> >> > >> >> >> > I have run csg_dump --top topol.xml >> >> >> > >> >> >> > to check the mapping. The problem is that for my water beads, it >> >> >> > seems >> >> >> > like >> >> >> > votca has reopened the pdb file as the index starts from 0 and the >> >> >> > atom >> >> >> > types are incorrect despite the fact that I say first="51328" for >> >> >> > the >> >> >> > water. >> >> >> > >> >> >> > Is this the wrong way to declare multiple molecule types using a >> >> >> > pdb >> >> >> > topology? >> >> >> It looks ok to me, but without the pdb I cannot say much. Can you >> >> >> send >> >> >> PEO16-PBO22-FULL.pdb to [email protected] and I will have a look! >> >> >> >> >> >> Christoph >> >> >> >> >> >> > >> >> >> > I would be very grateful for any suggestions on this. >> >> >> > >> >> >> > Cheers, Dan. >> >> >> > >> >> >> > -- >> >> >> > 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 http://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 http://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 http://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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
