I guess the mapping xml for special exclusions might be needed with packages other than Gromacs. E.g. DL_POLY certainly does not provide an easy way of altering exclusion lists.
This remark is just for completeness of discussion... Andrey On Tue, Jul 24, 2018 at 1:47 PM, 'Andrey Brukhno' via votca < [email protected]> wrote: > > On Tuesday, July 24, 2018 at 12:48:40 PM UTC+1, Christoph Junghans wrote: >> >> 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: >> >> >> >> > >> >> > 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 >> >> > >> > 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 need a mapping file, is obsolete and got removed in: 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. >> > > For my current purposes (and I think generally) taking exclusions from a > special tpr file is more convenient. > It is also much less hassle to prepare, as well as to implement in the > workflows. > > >> > >> > 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. >> > > OK, I have to admit to using a wrong flag `--map' instead of `--cg' above. > With the correct flag the exclusions are calculated correctly based on > mapping xml file. > > Andrey > > >> 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 a topic in the > Google Groups "votca" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/votca/l42VuhKqQb4/unsubscribe. > To unsubscribe from this group and all its topics, 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. > -- 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.
