Dear Christoph, That's the answer I want, thank you so much again. Best regards, Zidan
On Sunday, April 10, 2016 at 4:08:43 AM UTC+2, Christoph Junghans wrote: > > 2016-04-09 15:55 GMT-06:00 Zidan Zhang <zhang...@gmail.com <javascript:>>: > > > 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); > Yes, the mapping can make a huge difference in the interactions and hence > IBI. > There was an interesting paper about the influence of mappings: > <http://scitation.aip.org/content/aip/journal/jcp/136/19/10.1063/1.4705420> > > > > 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.) > This really depends on your system. But I would start with trying to > separate bonded and non-bonded interactions.(see the 2009 Votca > paper). > Do a single chain in vacuum simulation, take the bonded distributions > from there Boltzmann invert them and just do IBI on the non-bonded > interactions while keep the bonded ones fixed. You can always do IBI > on the bonded interaction at a later stage as well if the > distributions aren't reproduces good enough. > > Christoph > > 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>: > >> > 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. > >> > To post to this group, send email to vo...@googlegroups.com. > >> > 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+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.
