2016-04-09 15:55 GMT-06:00 Zidan Zhang <[email protected]>: > 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 <[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. -- 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.
