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

Jinan Niu njn0516 at 163.com
Fri May 27 11:29:34 CEST 2011

Lemkul, thanks
At 2011-05-25 18:56:59,"Justin A. Lemkul" <jalemkul at vt.edu> wrote:
>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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