Cun Zhang wrote:
Hi,gmx users,
I want to set CNT infinite in the system of CNT and water. I'm using
GMX 4.1,so I have set pbc=xyz, periodic_molecules=yes in mdp file.
Not possible, Gromacs 4.1 hasn't been released :) If you're using version
4.0.1, you shouldn't, because it has a nasty bug that affects performance very
severely.
I set the box size larger than CNT's length a C-C bond(half up and half
down).
If I don't do a EM, it will crumble. But if I do it,it can't satisfy
that the box size is larger then CN't length a C-C bond.
I don't understand this. Are you getting any error messages? Screen and log
output are more useful in most cases.
I have searched google and gmx mail list, but still can't solve it .
I found that GMX online document about Carbon
Nanotube(http://www.gromacs.org/index.php?title=Documentation/How-tos/Carbon_Nanotube)
say,
Be absolutely sure that the "terminal" carbon atoms are sharing a bond
in the topology file.
I don't understand it.How should I do?
Make sure there is a bond in your topology between the appropriate atoms at one
"edge" of the box to the appropriate atoms at the other "edge" of the box.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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