2016-05-08 12:07 GMT-06:00 Zidan Zhang <[email protected]>: > Dear all, > I think I find the problem, it's the different between g_rdf and the > csg_stat, after reading several threads, I think it will converge. When I > get the new data, I will update this thread. Thank you! > g_rdf and csg_stat should give identical results if they don't than it is usually due to missing exclusions. However, if you are just doing IBI on non-bonded interactions (and not the bonded interactions), you don't need a 1:1 mapping file and VOTCA will read the exclusion directly from the tpr file.
Christoph Best, > Zidan > > > On Sunday, May 8, 2016 at 7:12:42 PM UTC+2, Zidan Zhang wrote: >> >> 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. > -- 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.
