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 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.
