Hi Christoph, Thank You for the fast reply. I just noticed the switch in the xy to yx coordinates when I convert from gro to gro by csg_map --cg .. --top ... --traj conf.gro --out conf_CG.gro for example. I did not check it for the traj.xtc files. But if I change the respective line in gmxtrajectoryreader.cc, the xy and yx coordinates do not chagne any more.
Best Christoph Am Freitag, 3. Juli 2015 22:23:39 UTC+2 schrieb Christoph Junghans: > > 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] > <javascript:>>: > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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.
