I nearly forgot to reply. The problem has been solved. It is due to a different representation of the box vectors in gromacs and in votca. In the newest stable version there is a separate groreader.cc in addition to the gmxtrajectoryreader.cc and the box representation in Votca correct.
Am Mittwoch, 8. Juli 2015 10:43:59 UTC+2 schrieb Christoph Junghans: > > > Am 07.07.2015 14:03 schrieb "Christoph Scherer" <[email protected] > <javascript:>>: > > > > 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] <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. > -- 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.
