On Friday, January 3, 2020 at 5:30:28 PM UTC+2, Christoph Junghans wrote: > > > > On Fri, Jan 3, 2020 at 8:13 AM CHRISTINA-ANNA GATSIOU < > [email protected] <javascript:>> wrote: > >> Hi Christoph, >> >> I have set all exclusions in the gromacs topology file. However, during >> IBI for one nonbonded interaction I get the attached distribution (red >> corresponds to the bond distribution the bonded beads, green corresponds to >> the target distribution of bead types and blue to IBI distribution at step >> 30). It seems that bonded pairs are included in the g(r) even though I have >> specified them as non interacting in the exclusion list. I cannot figure >> out what might be the problem here. Thanks in advance. >> > Go in the log file (usually inverse.log) and find the last csg_stat call > (e.g. with "grep csg_stat inverse.log") and post it here. > > csg_stat --nt 8 --options settings_nb.xml --top topol.tpr --trj traj.xtc --begin 5 --first-frame 0 --cg topology.xml;
> Christoph > >> >> >> Best regards, >> Christianna >> >> On Saturday, December 14, 2019 at 8:52:34 PM UTC+2, Christoph Junghans >> wrote: >>> >>> >>> >>> On Sat, Dec 14, 2019 at 11:27 CHRISTINA-ANNA GATSIOU < >>> [email protected]> wrote: >>> >>>> Hi Christoph, >>>> >>>> My topology.xml does contain exclusions. I have only specified nrexcl 3 >>>> which I thought should do the job. Do I need to specify exclusions in the >>>> topology.xml or in the gromacs topology file ? >>>> >>> If you are using a tpr file as topology VOTCA will read the exclusions >>> from there. If you are using a xml topology exclusions will be generated >>> out of the bonds and angles. >>> >>> Just look in inverse.log what topology file is used by csg_stat and run >>> csg_dump on it to check the exclusions. >>> >>> Christoph >>> >>>> Thanks for the prompt response. >>>> >>>> Best regards, >>>> Christianna >>>> >>>> On 14 Dec 2019, at 1:26 AM, Christoph Junghans <[email protected]> >>>> wrote: >>>> >>>> csg_dump --excl --top <topology_file> >>>> >>>> >>>> -- >>>> 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/7889732D-B264-4FBB-A951-271C1190FB7F%40gmail.com >>>> >>>> <https://groups.google.com/d/msgid/votca/7889732D-B264-4FBB-A951-271C1190FB7F%40gmail.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] <javascript:>. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/c927b5cc-550d-4388-b10f-ae598ec15753%40googlegroups.com >> >> <https://groups.google.com/d/msgid/votca/c927b5cc-550d-4388-b10f-ae598ec15753%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/92a68fed-7eca-41d6-90cb-f7825f229c82%40googlegroups.com.
