[gmx-users] genconf problem

[Mark Abraham]

ANINDITA GAYEN wrote:
> 
> 
> Dear all,
> I have download a POPG(lip 128+Na ion 128) bilayer from 
> "http://www.softsimu.org/downloads.shtml". I want to make a bilayer 
> containing 128 lip/leaflate i.e, with 256 lipids having suqre surface 
> area (X=Y). With the following commands :
> 1)"genconf -f popg.pdb -nbox 2 2 1 -dist 0 0 0 -o popc256.pdb"
> bilayer becomes 4 times larger with 512 POPG molecules (X=Y).
> 2)"genconf -f popg.pdb -nbox 2 1 1 -dist 0 0 0 -o popc256.pdb"
> bilayer becomes 2 times larger with 256 POPG molecules but, X=2Y.
> 3)"genconf -f popg.pdb -nbox 1 2 1 -dist 0 0 0 -o popc256.pdb"
>    bilayer becomes 2 times larger with 256  POPG molecules but, 2X=Y.
> please give me any suggestion how I can make a (11*11,i.e 242 lipids ) 
> or (12*12,i.e  288 lipids) bilayer from  (8*8,i.e  128 lipids)  POPG 
> bilayer.

Make a 16x16 bilayer, use a visualization program to identify atom 
numbers with physical location and then delete a suitable subset of 
molecules by hand in a text editor.

Mark