2015-11-12 0:15 GMT-07:00 Pallavi Banerjee <pallavis...@students.iiserpune.ac.in>: > 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? If you Boltzmann invert the rdfs you effectively turn the MARTINI potential into structure-based potential, don't do that.
Just use the force-field parameters from the MARTINI force field. In the spce/tf example we use a setup, which combined the standard spce force field with a course-grained one. You will have to do something similar. > > 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. Mixing structure-based and a free-energy based approaches sounds strange to me, it like mixing Steak and Ice cream, both are delicious by themselves, but together? On a side note, you could do a 4:1 mapping with IBI as well, if you have the rdf. Christoph > > > 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. -- 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 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.
