On Tue, Jul 24, 2018 at 1:34 AM, Christoph Junghans <[email protected]> wrote:
> On Mon, Jul 23, 2018 at 5:26 PM, 'Andrey Brukhno' via votca > <[email protected]> wrote: > > > > > > On Monday, July 23, 2018 at 8:18:39 PM UTC+1, Andrey Brukhno wrote: > >> > >> On Monday, July 23, 2018 at 3:17:49 PM UTC+1, Christoph Junghans wrote: > >>> > >>> On Mon, Jul 23, 2018 at 7:41 AM, 'Andrey Brukhno' via votca > >>> <[email protected]> wrote: > >>> > In this case, it's not an error message which is lost ;) Why does it > go > >>> > to > >>> > stderr at all? > >>> The code has the reason right there: > >>> #print this message to stderr because $(critical something) is used > very > >>> often > >>> > >>> > Moreover, if I try to run the iteration a second time, everything > >>> > including > >>> > errors is reported back > >>> Well that is good, nevertheless we just spend 5 E-Mails back and > >>> forth, hunting down a bug you introduced yourself. > >>> And I now recall you made that change to filter gromacs "Read frame > >>> XXX" message, which is fixed when using a newer gromacs version > >>> (>=2016.3), see: > >>> > >>> https://github.com/votca/csg/commit/155eb770873a6f65bac372c9f8c5ef > c9f3a4be75 > >>> > >>> > > >>> > Anyway, my primary issue is not about messages, but to make it work > >>> > correctly for distributions. > >>> Like I said in the other email if section 7.3.2 is right, a mapping > >>> file might be needed only for IMC, but even that I think is not true > >>> anymore in v1.3.1. > >> > >> > >> My test IMC iteration went through without tagging the 1:1 CG map file. > >> > >>> > >>> So you need to figure out, which exclusions you want to read the ones > >>> from the mapping file or the ones the tpr. > >>> For the former specify a mapping file or the latter don't. > >> > >> > >> OK, I preferred the exclusions from topol-rdf.tpr (which appears to work > >> now for IBI), so I skipped the map tags in my settings file for IMC too. > >> However, the distributions are still wrong in the case of IMC. > > > > > > As a matter of fact including a 1:1 topology xml where all the > > intra-molecular pairs are counted as bonded does not affect the exclusion > > list (so only tpr file matters) for csg_dump: > > > > 1) the case where topol.tpr has nrexcl = 3 and topol-map11-rdf.xml > defines > > all pairs as bonded > > > >> csg_dump --top topol.tpr --map topol-map11-rdf.xml --excl > > Reading file topol.tpr, VERSION 2018.2 (single precision) > > I have 12 beads in 1 molecule > > > > List of exclusions: > > 1 2 3 4 > > 2 3 4 9 > > 3 4 9 10 11 > > 4 8 9 10 11 12 > > 5 6 7 8 > > 6 7 8 10 > > 7 8 9 10 > > 8 9 10 11 > > 9 10 11 12 > > 10 11 12 > > 11 12 > > > > 2) the case where topol.tpr has nrexcl = 3 and no topol-map11-rdf.xml is > > used > > > >> csg_dump --top topol.tpr --excl > > Reading file topol.tpr, VERSION 2018.2 (single precision) > > I have 12 beads in 1 molecule > > > > List of exclusions: > > 1 2 3 4 > > 2 3 4 9 > > 3 4 9 10 11 > > 4 8 9 10 11 12 > > 5 6 7 8 > > 6 7 8 10 > > 7 8 9 10 > > 8 9 10 11 > > 9 10 11 12 > > 10 11 12 > > 11 12 > > 13 14 15 16 > > 14 15 16 21 > > 15 16 21 22 23 > > 16 20 21 22 23 24 > > 17 18 19 20 > > 18 19 20 22 > > 19 20 21 22 > > 20 21 22 23 > > 21 22 23 24 > > 22 23 24 > > 23 24 > > > > 3) the case where topol-rdf.tpr has nrexcl = 10 so all pairs within a > chain > > are excluded from RDF calculation > > > >> csg_dump --top topol-rdf.tpr --excl > > Reading file topol-rdf.tpr, VERSION 2018.2 (single precision) > > I have 12 beads in 1 molecule > > > > List of exclusions: > > 1 2 3 4 5 6 7 8 9 10 11 12 > > 2 3 4 5 6 7 8 9 10 11 12 > > 3 4 5 6 7 8 9 10 11 12 > > 4 5 6 7 8 9 10 11 12 > > 5 6 7 8 9 10 11 12 > > 6 7 8 9 10 11 12 > > 7 8 9 10 11 12 > > 8 9 10 11 12 > > 9 10 11 12 > > 10 11 12 > > 11 12 > > > > I am quite sure what you want to tell us with that comparison! If you > want to achieve the same as nrexcl=10 with a mapping file, you will > need to add 12*11/2=66 bonds between all possible pairs to that > mapping file. > > Christoph > This is why I preferred to use topol-rdf.tpr and not the mapping xml file. But since you suggested that a mapping file might be needed in some cases, like IMC with bonds, I tried that as well. But apparently mapping file does not affect the exclusions at all (there is no difference for my two mapping files)! The bottom line here: adding bonds for all pairs in mapping file does not affect the exclusion list at all - it does look like exclusion list comes from tpr only. I am stopping now testing this, because the workflow works now for me, with my modifications in mc_stat_generic.sh Andrey > >> > >> > >>> > >>> > -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
