Hi, 2015-06-24 13:47 GMT-06:00 Vitalie Botan <[email protected]>: > Hi there, > > I am trying to adopt KB-IBI method for a dilute polymer system with implicit > solvent. Since the system is very dilute (only 3 polymers in a water box), > the corresponding RDFs don't show any plateau in the long range in both AA > and CG models. This fact poses the main problem in the standard IBI scheme - > convergence is inherently slow and the relative error never gets better than > 15-20%. The idea is to refine the best CG-approximation with the KB-IBI > method to minimise the error at least to the values below 10%. > I have few questions regarding the theory of KB-IBI implementation in VOTCA > (I guess it's based on the JCTC paper from 2012) and some technical > questions about its use with LAMMPS: > 1) in the numerical integration of eq.1 (JCTC 2012) the cutoff value is the > same as ramp-cutoff or they are unrelated? In my case I guess I have to use > the same value of the cutoff; They can be different, however the kb intergral depends on the rdf, so if the ramp cutoff (inverse.post_update_options.kbibi.r_ramp inside the non-bonded block) is bigger than max it becomes the same as max efficiently.
> 2) the start and stop values for Gij averaging is defined as a plateau > "width"? Yes width = stop - start > 3) the prefactor A value has to be converted to the corresponding units (i.e > kcal/mol/angstrom)? My understanding is that it can be taken more or less > arbitrarily. Yes. We call it educated guessing. > 4) how is the integral correction defined? Not sure what your question is! Christoph > > I would appreciate any hints or suggestions. > Best regards, > > Vitaly > > > -- > 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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
