On Tue, Apr 7, 2020 at 9:59 AM Wolfgang Verestek < [email protected]> wrote:
> Dear Christoph, > > thanks for your fast response. i followed you suggestion, renamed the > files and added the box tag to the topology file (files attached). But the > result stays the same. So, as you said that gromacs format is better > supported i changed my output to gro87 format. No errors, but the > discrepancy remains, regardless if i'm using wrapped or unwrapped coords in > the conf.gro file. See below. Are there any other things i could change? > Another format? > Is it possible to set the boundary conditions somewhere specifically? Or > could it be that periodic images of the specific atoms are ignored (the > simulation box is kind of small and close by region seems ok)? > Sorry, I didn't have time to look at your files yet, but does OVito handle exclusion in the same way as VOTCA? Have a look at the output of "csg_dump --top topology.xml --excl" Secondly you could use "csg_map --top topology --no-map --trj lammps.dump --out out.pdb", to check if the coordinates are read correctly. Christoph > > Is there a way to visualize the xml or gro files? I know vmd, but that > segfaults when reading the gro file. > > Ultimately the whole thing should go into force matching. But i guess the > results will be off if already the RDF is wrong? > > Is it really necessary to have one file per molecule type and what > distinguishes different molecule types? If i have several PA6 molecules > with different length/count of monomers is that already different molecules? > > Thanks and regards > Wolfgang > > > > -- > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/b4b7484f-2663-4fe6-a082-ad3c2ca1ef20%40googlegroups.com > <https://groups.google.com/d/msgid/votca/b4b7484f-2663-4fe6-a082-ad3c2ca1ef20%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e4ooWcCEYOBQhC_T-dVr-%3DAL6%2BJKcAvRzMV1dtdza-MVg%40mail.gmail.com.
