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; 2) the start and stop values for Gij averaging is defined as a plateau "width"? 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. 4) how is the integral correction defined?
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.
