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. 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]. > 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/CAHG27e5%3DmokHAcfAv0pXTC8UcfMuAjZZ7enj7TQyY7ZNoUub7A%40mail.gmail.com.
