Dear Gromacs Users!
I want to study dynamics of solvent burried into the protein interiour during simulation (to check solvent accessible area of different amino acid of my protein). Eg while simulating of Green Fluorescent protein I'd like to check how much water burried into the beta-can interiour of that protein ( which can effect chromophore of that protein for instance). What Gromacs utilites can be suitable for such analysis? I've tried to make such study with the g_rdf but I'm not quite sure about suitability of that tool for my task ( e.g what is the ref_group as well as first group about which program ask me when i tried g_rdf -f wild_Chimera_15ns.xtc -s minim.tpr -n index.ndx -cut 0.4 ) ? Thanks for help James -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
