Gavin Melaugh wrote:
Hi Justin
By "broken" do you mean split at the edge of the periodic box? If so
then yes.
Then that's your problem.
-Justin
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Hi
I have installed the new version of gromacs and so far I only use it as
a check when running grompp as it gnerates more information about cut
off charge group radii etc.
For a system of 256 hexane molecules in a cubic box I get the following
error.
WARNING 1 [file pbc.mdp]:
The sum of the two largest charge group radii (5.231524) is larger
than
rlist (1.700000)
This doesn't even make sense since my as system itself fits in a 3.2 nm
cubic box. I am pretty sure my topology is correct. I have seen on the
mailing list that there have been problems with this but they have all
been for bigger molecules.
Are any of the molecules broken? That was the exact case just a
couple of days ago:
http://lists.gromacs.org/pipermail/gmx-users/2011-January/057980.html
-Justin
Gavin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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