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
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.
