Dear Christoph, Thank you very much for your reply! g_rdf and csg_stat indeed give the identical results. As shown in the attached figure, I have defined several dihedrals, but even I have 40000 frames (totally run 200 ns), the distributions don't look well, so I decided not to use dihedrals. But the RDFs were generated with the setting.xml file in which the dihedrals were defined. When doing IBI for nonbonded interactions, I wrote a <map> tag in the setting.xml file in which I have deleted these dihedrals (as shown in the earlier attachments), so that's why I have different results and the nonbonded interactions don't converge. Now I know the reason and IBI works fine. It's my mistake. Thank you again! Best, Zidan
<https://lh3.googleusercontent.com/-NYso0_SMnl4/VzD7iFug1UI/AAAAAAAAANQ/9k9r2ToB7Jc8pi8LfSVsmLfH3UEIYly9ACLcB/s1600/dihedral.png> On Sunday, May 8, 2016 at 10:44:52 PM UTC+2, Christoph Junghans wrote: > > > > 2016-05-08 12:07 GMT-06:00 Zidan Zhang <[email protected] <javascript:>>: > >> 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] <javascript:>. >> To post to this group, send email to [email protected] <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 [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.
