Okay, I'll expound more on this. Yes, I want to do IBI on the polymer-polymer interaction only, while keeping water-water and polymer-water interactions fixed. I do a separate purely MARTINI run with both the polymer and water in the system. I obtain rdfs of W-W and polymer-W from this MARTINI run . I invert these potentials and provide them as a tabulated input to VOTCA. Does this sound too odd or reasonable?
I am combining a structure-based and a free-energy based approach here because when it comes to an aqueous system the free energy of solvation matters a great deal, which should be taken care by MARTINI. Also, MARTINI provides a 4:1 mapping for water, which is an appealing level of coarse-graining. Thanks for your time! -Pallavi Banerjee On Tuesday, November 10, 2015 at 8:24:18 PM UTC+5:30, Pallavi Banerjee wrote: > > Hello, > > I am trying out this new method of integrating MARTINI and IBI. This is > because mine is an aqueous system and MARTINI water follows a 4:1 mapping > as opposed to IBI which limits you to a 1:1 mapping for water. The idea is > to perform IBI on just polymer-polymer interactions while keeping the > potential of interactions of water-water and polymer-water fixed. I obtain > these aforementioned potentials from rdfs of separate MARTINI runs, which I > plan to provide as input. I am unable to figure out a way to instruct VOTCA > to take these potentials as they are. > > Any help is appreciated. > > -Pallavi Banerjee > -- 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
