Hi Christoph, thanks for you bug report. I am not using non-orthorombic simulation box a lot, so there might be some things switched in the code. However, gro files aren't actually read through gmxtopologyreader.cc, but groreader.cc and the same for gmxtrajectoryreader.cc. This is mainly to allow to use gro files, which are nicely human readable, without having to build against libgromacs, which is useful when using lammps.
So in which cases do the xy and yx values get switched? A xtc to gro conversion or gro to gro? Cheers, Christoph 2015-07-03 9:51 GMT-06:00 Christoph Scherer <[email protected]>: > I found a possible bug in the library file gmxtrajectoryreader.cc in > votca-csg/scr/csg/libcsg/modules/io. > > There in lines 75 and in lines 132 it could be that m[i][j] = > _gmx_frame.box[i][j]; instead of m[i][j] = _gmx_frame.box[j][i]; is correct > and a possible index switch occured. > > I am not sure about this. However, when reading in a conf.gro file with > non-orthorombic simulation box, the original indices leads to a CG conf.gro > file where the xy and yx values are switched! > > (Could it be that in gmxtopologyreader.cc a similar error occured in line > 156 (m[i][j] = gbox[i][j]; instead of m[i][j] = gbox[j][i]; would be > correct?) I didn't check this. > > Cheers > > Christoph > > -- > 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.
