On Wed, Jan 8, 2020 at 02:56 CHRISTINA-ANNA GATSIOU < [email protected]> wrote:
> 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. > It depends, a mapping file is usually only needed if you want to do IBI on the bonded interactions as well. As VOTCA has no concept of nrexcl in gromacs once you map, you might need to more unphysical bonds, e.g. using a tpr with a chain with bonds A-B-C, A & C would be excluded if nrexcl is 2, after mapping A & B as well as B & C are excluded, but A & C are not, so you will need to add an unphysical bond between A & C to achieve that. Looking at the output of “csg_dump —excl —top topol” vs. “csg_dump —excl —top topol.tpr —cg map.xml” should reveal that. Can you send your tpr and mapping files? > > > > 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]> 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/c352c13c-4676-4b79-a75b-ddaa44ab9919%40googlegroups.com > <https://groups.google.com/d/msgid/votca/c352c13c-4676-4b79-a75b-ddaa44ab9919%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/CAHG27e5H6vAA3w0PoJPfzVLHaA9LpNa0K3ggu3dGfJb3Be%3Dpng%40mail.gmail.com.
