[gmx-users] Re: insert silicon atoms into ice structure (Justin A. Lemkul)

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 4 04:20:10 CEST 2010

Santan William wrote:
> Thanks for reply. 
> I intended to add some silicon atoms just into ice structure, so the 
> simulation box only containing ice. You said there probably isn't enough 
> space for them in the box. Did you mean I can't insert these atoms into 
> ice structure if the box only containing ice?

Well, are there cavities in the ice structure sufficiently large to fit your 
silicon atoms?  Judging by the failure of your approach, I'd say there's not.

> Is there any other way to insert silicon atoms into a solid ice structure?

You could try generating some random configuration of silicon atoms, then:

genbox -cp si.pdb -cs ice.pdb

You would then, of course, be potentially interrupting the lattice of water 
molecules if some are deleted due to overlap with your silicon atoms.  But as 
for whether or not that's important, you'll have to decide.


> Thanks a lot.
> Best,
> william
> Santan William wrote:
>>  Dear GMXusers,
>>          I wanna insert several silicon atoms into an ice crystal. I use
>>  genbox with a Silicon.pdb, but there's no any silicon atom in the out
>>  file. Do I miss anything? Anyone has some comments? Thanks a lot.
> If zero atoms were inserted, there probably isn't enough space for them 
> in the box.
> -Justin
>>  Best,
>>  william


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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