On Tue, Jul 24, 2018 at 2:31 AM, 'Andrey Brukhno' via votca <[email protected]> wrote: > > > 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/155eb770873a6f65bac372c9f8c5efc9f3a4be75 >> >>> >> >>> > >> >>> > 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)! Just to clarify, the section 7.3.2 of the manual, which suggest you need a mapping file, is obsolete and got removed in: https://github.com/votca/csg-manual/pull/8. Mapping files are only implemented for RDF calculations for IBI (and the optimizer) at this point and aren't used for methods like IMC and RE. It would be easy to add, but nobody has asked for it yet.
> > 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. Sorry, but that statement is just wrong, but must have made a mistake in your mapping file. VOTCA reads the exclusions from the topology file (tpr, xml or whatever), but if a mapping file is specified a mapping is done (1:1 or not) and after the mapping exclusions get re-generated from the bonded interactions in the mapping with an "nrexcl=1"-like algorithm, i.e. beads in a bond, angle or dihedral are excluded. One can test that very easily using the "hexane/ibi_all" example: These are the exclusions in the tpr (from step_001): $ csg_dump --top topol.tpr --excl | head -5 I have 3000 beads in 1000 molecules List of exclusions: 1 2 3 2 3 Using the included mapping file with 2 bonds and 1 angle, one can get the same exclusions: $ csg_dump --top topol.tpr --excl --cg ../hexane_cg.xml | head -6 I have 3000 beads in 1000 molecules I have 3000 beads in 1000 molecules for the coarsegraining List of exclusions: 1 2 3 2 3 When removing the angle from the mapping file, one get less exclusions: $ csg_dump --top topol.tpr --excl --cg ./hexane_noangle.xml | head -6 I have 3000 beads in 1000 molecules I have 3000 beads in 1000 molecules for the coarsegraining List of exclusions: 1 2 2 3 When removing the bonds and angle from the mapping file, one get no exclusions: csg_dump --top topol.tpr --excl --cg ./hexane_cg.xml | head -6 I have 3000 beads in 1000 molecules I have 3000 beads in 1000 molecules for the coarsegraining List of exclusions: <nothing> So everything works like expected. However, you won't be able to use exclusions from mapping files out side of IBI anyhow. > I am stopping now testing this, because the workflow works now for me, with > my modifications in mc_stat_generic.sh The modification you did is already part of the current development branch since Aug 2017 and hence will be part of VOTCA v1.5. Christoph > > 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. -- 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 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.
