2016-04-09 15:02 GMT-06:00 Zidan Zhang <[email protected]>: > Dear all, > As mentioned in the title, does Votca support improper dihedrals in IBI > method? I have checked the manual, but found no answer. > When I include improper dihedrals into my system, the simulation box always > explode, the error message is general for GROMACS: "4 of the 14000 bonded > interactions could not be calculated because some atoms involved moved > further apart than the multi-body cut-off distance (1.20727 nm) or the > two-body cut-off distance (1.5 nm)". > But when I ignore the improper dihedrals, everything is OK for the IBI > iterations. Technically nothing prevents you from using improper dihedrals in VOTCA, but the above error looks like there is a problem in your setup. Before doing IBI you need to ensure that your setup works, you can do so by replacing the missing interaction by normal LJ ones and run it for a couple of hundred steps. Once you have a set of LJ interaction, which don't make your system explode, you can use these as initial guesses in IBI.
Christoph > Thank you very much! > Zidan Zhang > > -- > 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.
