Hi Sikandar Excuse me take the wrong file, by catching it quickly. You went right to the point, a point in parameter table is in "i" when must be "o", the border data, the problem was <= I change it, and runs fine. On my understanding is that "i" is in range, which means include in cubic b splines fitting. Thank you by your help
Best Regards Marc On Wed, May 7, 2014 at 11:35 AM, Sikandar Mashayak <[email protected]>wrote: > Hi Marc > > The inverse.xml file you have sent is actually the xml input settings > file. I was looking for the log-file > which contains the detailed output messages of running csg_inverse. > > Anyway, I am guessing the error "table_average.sh: averaging with awk > failed" may be due to > flags- mismatch between the initial parameter tables and step_002 > parameters. table_average > script computes the averages of CG potential parameters and tables. And by > default, it requires the > flags in all the rows of all the tables to match exactly. > > So, could you please make sure that in the initial parameter table all the > flags for r <= cbspl.min are set to 'o' > and the flags for r > cbspl.min are 'i'. You can refer to initial > parameter table and settings. > > Let me know if this solves the issue. If not please send me the > inverse.log the one I mentioned above. > > If you need, I can give you more information what are flags and why we use > them, once we take care your > issue. > > Thanks, > Sikandar > > > On Tue, May 6, 2014 at 7:27 PM, Marc Segovia <[email protected]>wrote: > >> Hi Sikandar >> >> Attached are inverse.log file and settings.xml files. >> Thank you >> Marc >> >> >> >> >> On Tue, May 6, 2014 at 9:02 PM, Sikandar Mashayak >> <[email protected]>wrote: >> >>> Hi Marc >>> >>> Can you please send inverse.log file? It will have more details about >>> the failure. >>> >>> Thanks >>> Sikandar >>> >>> >>> On Tue, May 6, 2014 at 5:40 PM, Marc Segovia <[email protected]>wrote: >>> >>>> Hi Sikandar >>>> >>>> You are right the rdf are converged in spce/water. >>>> >>>> Now I move to other model, I fit settings.xml script, include as guess >>>> a initial value from ibi previous, but an old problem appears. >>>> >>>> "table_average.sh: averaging with awk failed" >>>> >>>> I saw in mailing list, this is an issue related with a mismatch in >>>> param.cur, same happens in my case, steep-001 runs well, but in 002 >>>> colapse, both files mismatch, different number of parameters. >>>> >>>> My develpement version is 1.88, from 19.10.2013, maybe this wasn't >>>> solved yet , so I need to update my dev version ? >>>> >>>> >>>> Thanking in advance by your help >>>> >>>> Best Regards >>>> Marc >>>> >>>> >>>> On Sat, May 3, 2014 at 1:29 PM, Sikandar Mashayak <[email protected] >>>> > wrote: >>>> >>>>> Hi Marc >>>>> >>>>> Did you check the CG-CG RDF at 300the step? How do they compare with >>>>> the reference RDF? >>>>> >>>>> In my experience, I found that, in the case of bulk water, with the >>>>> current RE minimization method in VOTCA, >>>>> the CG potentials more or less converge to the values which reproduce >>>>> target RDF in less than 200 iterations. >>>>> However, due to statistical nature of short CG-MD simulations at every >>>>> update step, the values of CG potentials >>>>> fluctuate around the converged values. These fluctuations may or may >>>>> not satisfy the convergence check criteria, i.e., they may be smaller or >>>>> larger than the specified tolerance, and it depends on various setting >>>>> parameters such as length of CG-MD simulations, relaxation parameters, and >>>>> number of knot values. >>>>> >>>>> Therefore, it is always good to check the CG particle RDFs >>>>> periodically to judge whether the RE minimization is >>>>> converged or not. I guess, in VOTCA, there is a way to use CG particle >>>>> RDFs as a measure to decide convergence. I will check how to do that and >>>>> get back to you. >>>>> >>>>> We are also working on implementing alternative approach for RE >>>>> minimization, which is a deterministic approach. It is based on >>>>> reweighting >>>>> strategy. You can read more about it in the article >>>>> >>>>> Chaimovich, Aviel, and M. Scott Shell. “Coarse-Graining Errors and >>>>> Numerical Optimization Using a Relative Entropy Framework.” *The >>>>> Journal of Chemical Physics* 134, no. 9 (March 3, 2011): 094112. >>>>> doi:10.1063/1.3557038 >>>>> >>>>> I hope it helps. Let us know if you have any further questions or >>>>> suggestions. >>>>> >>>>> Thanks, >>>>> Sikandar >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Fri, May 2, 2014 at 4:31 PM, Marc Segovia <[email protected]>wrote: >>>>> >>>>>> Hi >>>>>> >>>>>> Last days I run relative entropy tutorial, using votca 1.3, in spce >>>>>> water model >>>>>> After several days in my PC, finally the cg don't converge. >>>>>> >>>>>> step 300 done, needed 1083 secs >>>>>> Doing convergence check: default >>>>>> Iterations are not converged, going on >>>>>> >>>>>> My question is , this happens because a convergence of 0.001 is to >>>>>> small, or because numerical errors in my software or because the number >>>>>> of >>>>>> configuration to average is too low , 50 ? or something else. >>>>>> >>>>>> Thanking in advance by your help >>>>>> >>>>>> Best Regards >>>>>> >>>>>> Marc >>>>>> >>>>>> -- >>>>>> 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 http://groups.google.com/group/votca. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> >>>>> -- >>>>> 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 http://groups.google.com/group/votca. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> -- >>>> 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 http://groups.google.com/group/votca. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >>> 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 http://groups.google.com/group/votca. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- >> 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 http://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. >> > > -- > 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 http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "votca" group. 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