Hi Justin, > In addition to that, you may consider using pbc = full to get an > infinite system and potentially avoid some of those edge effects it > looks like you are seeing. I know others have used that kind of > setup with carbon nanotubes (not my area of expertise, but I've read > the discussions).
Thanks a lot! That was a great tip! :) With the pbc = full setting I can use my topologies with bonds defined over the periodic boundaries without messing up the structure. I'll use the freezegrps additionally nevertheless because it speeds up the simulation and my substrate isn't supposed to move anyway, but with the 'full' option it would even work out without. I only wonder what's the difference between 'full' and 'xyz'? In the manual 'full' is not even mentioned and on the list archives I found several posts that tell that 'xyz' is a kind of optimization that does not work for infinite systems (hence my problems), and it could not be used with constraints in earlier versions, but now it's fine. Is there anything more I should know about the 'full' option, or why is it not listed in the run parameters section of the manual? Best regards, Michael -- http://www.defux.de _______________________________________________ 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
