Hello Charles, I have uploaded a file called charles.tar.gz under the login of santhu. Let me know if that did not work out or any other comments.
Thanks Santhosh On Wed, Sep 11, 2013 at 10:00 AM, Charles Schwieters <char...@schwieters.org > wrote: > > Hello Santhos-- > > > > > My concern is this : > > > > The force on the conformation whose weight is 0.1 is too low to drive it > to > > the minimum. The possible solution is that increase the force constant by > > using rdc.setScale or something similar but that would mean the > conformation > > with weight 0.9 would have a large force and am not sure if that would > not > > cause any problems. The multiplication of the weight factor might cause > > problems in setting the right force constant. > > The prefactors for each ensemble contribution is what it is, and > changing that in the gradient calculation will only cause a worse > minimum to be obtained (because the gradient would be incorrect). > > > > > While what is being done is mathematically correct, in my > > experiments the protocol did not work well. We took 2 distinct > > conformations of a protein and assigned them weights of 0.8, 0.2 > > while generating the artificial RDC's and NOEs from those. When > > starting with the global minimum [the original 2 conformations with > > weights of 0.8, 0.2], the second member moved away from the global > > minimum. [I hope I was clear in my explanation, please ask if > > something is not clear]. > > > > ok. That means that something is wrong or not accounted for. I'm happy > to help if I know more details. You might upload a complete example > which shows the poor behavior here (after logging in): > > http://nmr.cit.nih.gov/xplor-nih/download.cgi > > best regards-- > Charles >
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