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

Justin A. Lemkul jalemkul at vt.edu
Wed May 25 12:56:59 CEST 2011

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.


> --
> 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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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