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.
