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Joined: Jul 2006
Posts: 118
B
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B
Joined: Jul 2006
Posts: 118
Hi, All,
The add-ions.str need to setup crystal, may I know what does this mean, where can I find a template of cryst.str?
===============================================================
! SETUP CRYSTAL (DEFINE, BUILD), IMAGE CENTERING W. MODIFIED PSF
stream cryst.str
===============================================================

Thanks


Regards BioStanley -----------
Joined: Sep 2003
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rmv Online Content
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It's highly system dependent; for a tetragonal prism of lipids and water in a bilayer configuration--

* setup simulation cell via crystal for DPPC bilayer
*

calc xy = sqrt( 40. * 64. ) ! CELL EDGE; NAGLE BBA 64 A**2 PER LIPID
set z 65.8855 ! Z HEIGHT
crystal define tetragonal @XY @XY @Z 90. 90. 90.
crystal build cutoff 25. noper 0
! IMAGE CENTERING BY RESIDUE
image byres

return

while for a large solute in a rhombic dodecahedron

* rhdo with 60 dpc micelle in water
*

set a 69.68905
crystal define rhdo @A @A @A 60. 90. 60.
open unit 1 read card name ../rhdo.cry
crystal read card unit 1
close unit 1
image byres sele .not. segid B end
image byseg sele segid B end

return

In the latter case, rhdo.cry is a crystal transformation file made with CRYSTAL BUILD followed by CRYSTAL WRITE; with this file, CRYSTAL BUILD is replaced by CRYSTAL READ.

For more info, see crystl.doc


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