2016-04-09 16:38 GMT-06:00 Alireza Moradzadeh <[email protected]>: > I looked at simplex tutorials. I don,t now why we need n+1 line, n+1 sets is a requirement of the simplex algorigtm, see our recent paper: <http://dx.doi.org/10.1371/journal.pone.0131754> or <https://en.wikipedia.org/wiki/Nelder%E2%80%93Mead_method> > furthermore, when i tried to run my settings.xml based on the a combination > rule I got the error mentioning there is no parameters for > interaction between two beads. I am trying simplex on a four bead model so I > don't have enough parameters to allocate for all of the > interaction. Like I said in my last email you need at least one parameter per interaction, you have 3 interactions and 4 parameters so you should be fine. However looking at the code, I think it could be rewritten to list this constraint.
Christoph > >> On Apr 9, 2016, at 2:49 PM, Christoph Junghans <[email protected]> wrote: >> >> 2016-04-08 22:26 GMT-06:00 Alireza Moradzadeh <[email protected]>: >>> By the way I would be glad if you could provide more information on how to >>> choose parameters initials >>> I could not find so much information on how I should choose those value or >>> even its organization >> Have a look at the methanol-water simplex tutorial there is a >> simplex.in file for each interaction. >> The values in there are given in the same order as in the xml file. >> You will need n+1 sets to start with (lines in simplex.in) These sets >> can be generated by randomly perturbing some values from a single set, >> which you got from e.g. fitting an IBI potential. >> >> Christoph >> >>> >>> Thanks, >>> Alireza >>> >>> >>>> On Friday, April 8, 2016 at 10:21:23 PM UTC-5, Alireza Moradzadeh wrote: >>>> >>>> Thank you for your answer. >>>> >>>> I am also wondering if there is a way to keep eps and sigma positive >>>> during simulation time. Because the optimization method is blind to >>>> physical >>>> meaning of eps and sigma I got negative value using other methods in votca >>>> package. >>>> Is it possible to enforce this condition using this method or RE. Also is >>>> there anyway in votca package to treat charge of beads as a variable during >>>> simulation so I could control sigma and epsilon by variable charge. >>>> >>>> Thanks, >>>> Alireza >>>> >>>> >>>>> On Friday, April 8, 2016 at 4:04:48 PM UTC-5, Christoph Junghans wrote: >>>>> >>>>> 2016-04-07 19:10 GMT-06:00 Alireza Moradzadeh <[email protected]>: >>>>>> Dear VOTCA Users, >>>>>> >>>>>> >>>>>> For a system composed of two beads , I want to optimize pressure and >>>>>> interaction based on RDF but I want to stick to Lorentz-Berthelot >>>>>> combination rule. I want to know if I define my function as follows >>>>>> would it >>>>>> be right or not? and should I define pressure as target in each >>>>>> interaction. >>>>> Parameters are always global so, you should not list any parameter >>>>> twice, but you need to list at least one parameter for each >>>>> interaction. >>>>> e.g. list eps1 sig1 for CG1-CG1, eps2 for CG1-CG2 and sig2 for CG2-CG2 >>>>>> >>>>>> CG1-CG1 >>>>>> target rdf presssure >>>>>> function 4*eps1*[(sig1/x)**12-(sig1/x)**6] >>>>>> parmeters eps1 sig1 >>>>>> >>>>>> CG1-CG2 >>>>>> target rdf pressure >>>>>> function 4*(eps1*eps2)**2*[((sig1+sig2)/2/x)**12-(sig1+sig2)/2/x)**6] >>>>> This should be square root and not Power 2. >>>>> >>>>> Christoph >>>>>> parameters eps1 sig1 eps2 sig2 >>>>>> >>>>>> >>>>>> CG2-CG2 >>>>>> target rdf presssure >>>>>> function 4*eps2*[(sig2/x)**12-(sig2/x)**6] >>>>>> parmeters eps2 sig2 >>>>>> >>>>>> Thanks, >>>>>> >>>>>> -- >>>>>> 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 a topic in the >> Google Groups "votca" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/votca/ISshiaVA4mc/unsubscribe. >> To unsubscribe from this group and all its topics, 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. > > -- > 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. 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