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.
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] <javascript:>> 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] >> <javascript:>> 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] <javascript:>. >> 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]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/c927b5cc-550d-4388-b10f-ae598ec15753%40googlegroups.com.
