Dear Christoph Thank you so much for the answer, I will try it. I have two further questinos: 1. Does the mapping scheme influence the IBI iterations? When I separate -OH and -C6H4 as two beads (there are other beads like -(CH2)4 and -COOH), the system may crash during the MD, and I need a very small time step to keep the MD run stable (0.00002 ps), but when I treat -OH and -C6H4 as one bead, everything is fine (time step is 0.002 ps); 2. Can I just ignore the improper dihedral, and using only bond, angle and nonbonded interactions, are they enough to maintain the structure as its target atomistic structure? All the interactions are tabulated. (I have checked the distributions of impropers during the iteration, the peak positions are the same to the target distributions, but the peak intensities are different.) Best regards, Zidan
On Saturday, April 9, 2016 at 11:26:38 PM UTC+2, Christoph Junghans wrote: > > 2016-04-09 15:02 GMT-06:00 Zidan Zhang <zhang...@gmail.com <javascript:>>: > > > 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 votca+un...@googlegroups.com <javascript:>. > > To post to this group, send email to vo...@googlegroups.com > <javascript:>. > > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
