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.
