> I noticed that calculating the contact between the structural > ions in a protein with protein itself (the oxygen atoms > actually) the rdf does tend to 0 (at 6 nm it is 0.574 but it > seems going down) rather than 1. Could it be explained with > the fact the I am calculating the rdf on a non-homogeneous > situation?. In few words, after few nm there are not oxygen > atoms interacting with the ion.
Yes, that is typically the reason, it is an aggregated type of system, with essentially no or significantly less atoms in the bulk. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
