On Fri, Nov 16, 2018 at 6:30 PM Lee <[email protected]> wrote: > > Thanks for your reply. The attached files are the new rdf of the last > iteration step with target rdf distributions. Is the trend correct? Does it > converge if the iteration isn't interrupted? And do you have any suggestions > of my setting file? Such as the postupdate options, or postadd options which > can help it converges quickly.
Looking at the pictures, it seems some layering is going on. So I would have a look of the MD movie to see if something strange going on. Otherwise scaling the update might me a good idea, plus only updating one interaction per iteration step. Christoph > Thanks again > > 在 2018年11月17日星期六 UTC+8上午12:58:44，Christoph Junghans写道： >> >> On Fri, Nov 16, 2018 at 6:23 AM Lee <[email protected]> wrote: >> > >> > Hello votca users >> > I‘m trying to get the cg potential of DGEBA using IBI method. One dgeba >> > molecular is coarse grained with 3 beads, named as C A C. So in this >> > system, there are two types of beads (C and A), one type of bond (C-A), >> > one type of angle (CAC) and three types of non bonded interaction (CC, AA, >> > CA). These target distributions and CG model are all obtained from lammps >> > dump file manually. All of these target distributons have been smoothed. >> > Firstly, I do the ibi for all objects in order to get the bonded potential >> > table from step_001. Then, I just do the ibi process for non bonded >> > interaction. But with the process of iteration going on, the error "Pair >> > distance < table inner cutoff" occured during the MD simulation by LAMMPS. >> > And the rdf seems not to converge. I have tried several times with >> > different parameter for <table_begin>, but the error still occurs at some >> > iteration step. The configuration dump from lammps shows that some beads >> > get together, which is unnormal. >> > The attached files are the setting files and target distributions. Can >> > somebody point out my mistake? How could I modify my setting file? >> > I would really appreciate your advise. Thanks in advance! >> It seems you are doing things pretty correct already, sometimes it >> helps to add an additional purely repulsive interaction in LAMMPS to >> prevent close contacts ("Pair distance < table inner cutoff"). >> >> Christoph >> > Lee >> > >> > -- >> > 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.
