I looked at simplex tutorials. I don,t now why we need n+1 line, 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.
> 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.
