On Tue, Jul 24, 2018 at 6:52 AM, 'Andrey Brukhno' via votca <[email protected]> wrote: > 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. Another options to use an xml topology, which Jakub has implemented (see end of section 3.3), for the rdf calculation. This works with any simulation backend even when Gromacs support isn't compiled in.
Christoph > > 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 need a mapping file, is obsolete and got removed in: 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. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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