How can i impose absolute value selection on my simulation. By the way, using sigma and epsilon there is no need for table, wouldn't it be better to change topology file at each step. So implementation of combination rule would be automatic. I already wrote a simple scripts to do this after each iteration but it has some limitation for example i have to run my setting file step by step. This approach slow downs my work.
Alireza > On Apr 9, 2016, at 2:43 PM, Christoph Junghans <[email protected]> wrote: > > 2016-04-08 21:21 GMT-06:00 Alireza Moradzadeh <[email protected]>: >> 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. > No, we haven't implemented any range restrictions for simplex. For RE > I am not sure but Sikandar will know. > However you could just use the absolute values of eps and sigma in the > parameterization of the interaction, which will effectively force them > to be positive. > > Christoph >> >> 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.
