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.
