Michael Hirtz wrote:
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?
Indeed, it's a little strange that pbc = full does not appear in any official
documentation. Come to think of it, I can't remember when I first actually
learned about it myself :) The difference is that pbc = xyz is your standard
3-dimensional PBC option, but pbc = full is for molecules that repeat across
periodic boundaries (i.e., an infinite CNT, or the bonds within your graphite
sheet that are between atoms on opposite "sides" of the box).
-Justin
Best regards,
Michael
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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