Albert, 2017-10-01 3:20 GMT-06:00 Albert Solernou <[email protected]>: > Hi Cristoph, > thanks for your reply, and for pointing to the code, and sorry I forgot to > attach the messy output. It is now attached, as well as the conflicting .tpr > obtained just following the previous notes. > > It would be great to know what do you think of it. Sorry, but what kind of output are you expecting? In your "csgDump_interface" atomtypes seem to be consistent with the atom names, same for the masses.
And have you checked that "gmx dump" outputs the right number? Plus, could you make a simple system with just 2 residues exhibit the same misbehavior? (That would be easier to us to debug.) Christoph > > Thanks, > Albert > > > > On Friday, September 29, 2017 at 9:58:06 PM UTC+1, Christoph Junghans wrote: >> >> Hi Albert, >> >> 2017-09-28 6:24 GMT-06:00 Albert Solernou <[email protected]>: >> > Hi All, >> > I think that there is a bug in csg_dump, as it dumps wrong atom types >> > and >> > some wrong numbers when working with some modified tpr files. >> Can you be a bit more explicit which numbers are wrong? >> >> > >> > Not sure how much the bug affects my work, but feel I should report it >> > anyway. I attach clear instructions on how to get the bug, as well as >> > two >> > input files and the wrong output of the csg_dump. I can send the whole >> > set >> > of files but it is 145M. >> > >> > Could you please have a look at this? >> When csg_dump reads tpr files it uses Gromacs' libgmx, so the first >> step would be to run "gmx dump" on your tpr files and check if the >> same "wrong numbers" show up. >> Honestly VOTCA's wrapper around libgmx is very thin, see: >> >> <https://github.com/votca/csg/blob/master/src/libcsg/modules/io/gmxtopologyreader.cc#L93> >> >> Christoph >> > >> > Many thanks, >> > Albert >> > >> > -- >> > 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. -- 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.
