2015-04-27 4:10 GMT-06:00 Jakub Krajniak <[email protected]>: > Dear all, > > I have noticed that the latest development version (91580e26a728) behaviour > in different > way than the previous development version (52acb2010494). > Mainly I have single 3 beads molecule (hexane) A1-B1-A2 with bonds A1-B1, > A2-B2 and angle A1-B1-A2; > I expected that csg_stat will not produce any distribution for A-A, A-B, B-B > for this single molecule because > of defined bonds and angles between those beads. But the latest version > produce some peak in A-A and A-B. > Peak of A-B is in the same distance as the bond length A-B so it seems that > it is not an numerical error. > B-B did not show any peaks as expected. > > I have tried to add dummy bond 'A1-A2' in mapping but it didn't help. > > The only commit that recently play around exclusion list is this one > https://github.com/votca/csg/commit/19046906a6878aff61f14a06ebb1485a74c74f34 I reverted the merge for now, somebody will have to look into the exclusion scheme a bit more.
> > There is also a difference when I run csg_map --excl > previously: > @hpc-p-login-1 cg/prepare_single $ csg_dump --excl --cg hexane.xml --top > topol.tpr > Reading file topol.tpr, VERSION 5.0.4 (single precision) > I have 6 beads in 1 molecules > I have 3 beads in 1 molecules for the coarse graining > > List of exclusions: > 1 2 3 > 2 3 > 3 > > currently: > @hpc-p-login-1 cg/prepare_single $ csg_dump --excl --cg hexane.xml --top > topol.tpr > Reading file topol.tpr, VERSION 5.0.4 (single precision) > I have 6 beads in 1 molecules > I have 3 beads in 1 molecules for the coarsegraining > > List of exclusions: > 1 2 2 3 > 2 3 3 3 > > I am attaching distributions and xml files. > > Kind regards, > Jakub > > -- > 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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
