2015-05-21 8:35 GMT-06:00 Vitalie Botan <[email protected]>: > The results, however, look really odd. In my mapping file A-A beads are > always 1-3 neighbors apart from each, while A-B and B-B are bonded > directly. Those delta-like peaks in the RDFs could possibly result from not > being excluded properly? > It seems like there maybe some exclusions missing. Remember VOTCA used Gromacs-like exclusion scheme with nrexcl=1, meaning all atom involved in an bond, angle or dihedral are excluded.
You can check the exclusions with $ csg_dump --top XXX --cg YYY --excl and add more bonds to the mapping file to exclude more atom. Christoph > > > <https://lh3.googleusercontent.com/-CetzAvMmDZo/VV3s4VCH76I/AAAAAAAAAFo/1UgD3kl5-0M/s1600/B-B.RDF.png> > > > <https://lh3.googleusercontent.com/-bb38uUtVviI/VV3tAiwtk6I/AAAAAAAAAFw/OoREhuCYf7M/s1600/A-B.RDF.png> > > > <https://lh3.googleusercontent.com/-tZ1MZNImrH8/VV3sxofr1EI/AAAAAAAAAFg/XT0a5PvUbSg/s1600/A-A.RDF.png> > > > > -- > 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.
