Re: bks potential

From: sheida bagherzadeh (
Date: Sat Jul 06 2013 - 05:00:08 CDT

I have constructed my model that is consist of dna+graphene nanoribone
and amorphous sio2 or si3n4 as a substrate. system is solved in water.
I have constructed my model according to MODELING NANOPORE FOR
my substrate has hexagonal shape I write my basis vectors in config
file according to tutorial but when I run my model shape of water from
hexagonal changes to parallelpiped
(in inorganic builder when I choose si3n4 as a material and I set box
dimension of 15 15 1 the basis vectors are
113.925 0.0 0.0
56.96 98.66 0.0
0.0 0.0 2.902
but when I choose hegagonal box the basis vectors dont change and I
have used x and y basis vectors as cell basis vectors 1 and 2 in
config file and shape of water changes from hexagonal to parallepiped
with these babsis vectors )
Please guied me
Thanks a lot
Best regards

On 7/1/13, sheida bagherzadeh <> wrote:
> Hi
> I want to construct amorphous sio2 with bks potential I have done it
> with tutorial of nanopore modeling for dna sequensing when I run my
> simulation the error is:
> Expected 3 tabulated energy types but got 2
> I think my bks file have problem
> could you please guied me
> could you please introduce me a paper that explain annealing of sio2
> completely
> Thanks a lot
> Best regards

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