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] <javascript:>> wrote: > > > > > > On Tue, Jul 24, 2018 at 1:34 AM, Christoph Junghans <[email protected] > <javascript:>> > > 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 need a mapping file, is obsolete and got removed in: 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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.
