Hi Christoph, "Ok, if you are using a mapping file (--cg option), the exclusion from the tpr get mapped out." Does this mean that I should not be using the mapping file in order for the exclusions to be taken into account. I was under the impression that it was necessary. I have already defined those bonds in the mapping file. On Monday, January 6, 2020 at 8:34:01 PM UTC+2, Christoph Junghans wrote: > > On Mon, Jan 6, 2020 at 10:26 AM CHRISTINA-ANNA GATSIOU > <[email protected] <javascript:>> wrote: > > > > > > > > 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]> 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; > Ok, if you are using a mapping file (--cg option), the exclusion from > the tpr get mapped out. You will need to add bonds between the atoms > you want to exclude in mapping file. See here for an example: > > https://github.com/votca/csg-tutorials/blob/master/hexane/ibi_all/hexane_cg.xml#L25-L39 > > You don't need to do anything with these bonds in the IBI iterations. > > Again you can check the exclusions after mapping with csg_dump, e.g. > $ csg_dump --excl --top topol.tpr --cg topology.xml > > Christoph > > > > > >> > >> 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. > > > >>>> > >>>> -- > >>>> 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. > > > >> > >> > >> > >> -- > >> 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/92a68fed-7eca-41d6-90cb-f7825f229c82%40googlegroups.com. > > > > > > -- > Christoph Junghans > Web: http://www.compphys.de >
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