2016-05-09 15:13 GMT-06:00 Zidan Zhang <[email protected]>: > 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! > That is good news!
Beside doing bonded IBI there are only two cases when you want to use a mapping file: 1.) adding extra exclusion, which can also be done by using a special tpr file for the rdf calculation (in xml: cg.inverse.gromacs.rdf.topol). 2.) Make csg_stat calculate bonded distributions so that you can check with get perturbed. Christoph > 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]>: >> >>> 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. > -- 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.
