[gmx-users] what's the philosophy of -ci option in "genbox"?

[Justin A. Lemkul]

牛继南 wrote:
> Hi，gmx users:
> Recently, I have a question——what's the philosophy of -ci option in 
> "genbox"?
> My understanding is that a molecule is randomly generated in the hole at 
> first, then a new location around the molecule is generated according 
> to  a random seed , then gmx checks whether solve 
> or solute molecules will overlap, and so on. What is correct?
> 

A random location is generated, and the position is accepted if there is no 
overlap with nearby molecules.  See the insert_mols() function in gmx_genbox.c.

-Justin

> --
> Sincerely yours 
> Dr Ji-Nan Niu 
> School of Materials Science and Engineering.
> China University of Mining and Technology.
> Jiangsu Province, XuZhou 221116
> P. R. China
> _____________________________________________________
> Email: njn0516 at cumt.edu.cn <mailto:njn0516 at cumt.edu.cn> Phone: 
> +86-13852039305
> 
> 
> 

-- 
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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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