On Mon, Jan 6, 2020 at 10:26 AM CHRISTINA-ANNA GATSIOU <[email protected]> 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]. > 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 -- 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/CAHG27e7FAN-emBNhS9n-sQuiP5PjsiOFMPuYiYGUPQe%3Db9JSaA%40mail.gmail.com.
