On Thu, Apr 26, 2018 at 1:37 AM, Alexander Alexander <[email protected]> wrote: > > Dear all, > Using IBI over nonbonded parameters I intend to parameterize the CG > parameter for a molecule which has 3 beads in 2 types. The initial > CG-configuration.gro was extracted from the trajectory of an atomistic > simulation over the system which I am pretty sure that it has been enough > equilibrated with different ensemble and for enough computational time as > all of its properties are being stable by time. Even in each CG step I do > the minimization (pre.simulation). However, the CG nonbonded parametrization > crashes due to the issue of "1 of the 692 bonded interactions could not be > calculated because some atoms involved moved further apart than the > multi-body ...". Usually that error means your system is exploding. Have a look at the simulation movie with vmd. Try to replace the related bonded interaction with a potential with a stronger spring constant.
Christoph > I have been trying most of the suggested solutions for such an error, but no > success. I even reduced the number of beads from my initial mapping (5 > beads) to the current one (3 beads), but it crashes even earlier. > The materials for this system have been shared in the below link, I would be > so appreciated if you could kindly help me solve the problem. > https://drive.google.com/open?id=12VIJ3W9BgE0IlEls8ZlJ1uIAG3jqbNG0 > > Thank you very much. > > Best regards, > Alex > > -- > 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. 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.
