Dear Denis, Thank you for the reply, I have deleted the xtc file as listed in <cleanlist> section, I will re-run the last iteration to check RMSD. Sincerely, Zidan
On Sunday, May 8, 2016 at 7:03:32 PM UTC+2, Denis Andrienko wrote: > > Hi, > > IBI requires canonical sampling of the coarse-grained radial distribution > function. > Can you check if your system is still in a liquid state (i.e. not in a > glassy one)? You can do it by calculating RMSD of last iterations and > checking if a molecule diffused more than its own size. If not, you might > want to increase the runtime of every IBI step. > > In some exotic cases you just have to do more IBI steps. > > Best, > Denis > > On Sunday, May 8, 2016 at 3:53:32 PM UTC+2, Zidan Zhang wrote: >> >> Dear all, >> When optimise the nonbonded interactions, some of them don't converge, >> like shown in the picture. The system is a bulk system and has no crystal. >> I have tried several solutions: >> 1. change the scale factor (1.0, 0.7, 0.5); >> 2. change the initial guess by using high temperature (default 458 K, >> high T=600 K) in the setting.xml (nonbonded.xml as attached); >> 3. the order of optimisation. >> All of them have the same results. >> How can I solve this problem? >> Best regards, >> Zidan >> >> >> >> <https://lh3.googleusercontent.com/-eOfyHp6X1bg/Vy9Cx2MzKVI/AAAAAAAAANA/wuLn1LkrZOki0EIe1Gj2KyekymfeQmrjACLcB/s1600/rb-rb.png> >> >> >> >> -- 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.
