I have checked the exclusions and they seem to be ok, at least it works pretty well with the same mapping on the atomistic trajectory. I suspect it's purely numerical stability and convergence problems. In that respect I would like to ask you how the convergence criteria is actually defined in VOTCA, which functional form it takes (I couldn't find this information in the manual) and what is that damping parameter (eq. 2.15 of the manual) when doing updates, can it be controlled in the same spirit as Picard iteration scheme? I'm not sure what is the best way to iterate over multicomponent system: currently I update only single potential every single step, so that means that for one iteration only one convergence parameters should be checked. Is there also a way to control iterations with this parameter, i.e. to reject those updates, which lead to bigger convergence parameter?
--Vitalie On Thursday, May 21, 2015 at 7:45:33 PM UTC+2, Christoph Junghans wrote: > > > 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 > -- 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.
