Am 07.07.2015 14:03 schrieb "Christoph Scherer" <[email protected]>: > > 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.
Which version of votca is that? (See csg_map --help). Please ensure you are using 1.3-dev as I rewrote the gro topology reader in version 1.3. See < https://code.google.com/p/votca/wiki/Installing#Development_Version> on how to install it. Christoph > > 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]>: >> > 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. -- 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.
