2015-11-10 7:54 GMT-07:00 Pallavi Banerjee <pallavis...@students.iiserpune.ac.in>: > 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. That should be easy, VOTCA only does IBI on the interactions, which are listed in the settings file. Have a look at the propane/ibi example, there the bonded interactions are fixed, while the non-bonded ones are iterated via IBI.
In your case you will have to create a setup with all interactions being there except the polymer-polymer interaction. Due to the fact that Gromacs doesn't support mixing for tabulated and non-tabulated interactions, you will have to create table for the MARTINI interactions first, which should be too hard as it is just standard 6-12 LJ. Don't forget to add these extra force table to the filelist in the settings file. Christoph > > 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.
