[gmx-users] How to make a lipid bilayer with specific dimensions?

[Justin A. Lemkul]

NG HUI WEN wrote:
> Dear gmxusers,
> 
>  
> 
> I am trying to make a lipid bilayer with specific dimensions using 
> gromacs. So far, I have got up to:
> 
>  
> 
> 1)      Download a lipid POPC128a.pdb from Peter Tieleman’s website
> 
> 2)      Use genconf –f popc128a.pdb –o popcx2.pdb –nbox 2   2   1 to 
> multiply the lipid in the x and y axis. The resultant output was a lipid 
> with box vectors 12.478 ,   12.359 and 6.919 (nm)
> 
>  
> 
> My ultimate aim is to generate a POPC bilayer with the dimensions 
> 9.600   9.500 and 14.000. Currently, the lipid bilayer is too big. I 

Too big?  If you're using either of the two coordinate files above 
(popc128a.pdb, popcx2.pdb), they should be too small.

> would like to “crop” the excess lipids to the required size if at all 
> possible. I tried using editconf ( a bit of a long shot) to make a new 
> box size. The new structure file has a CRYST1 of 9.600   9.500 and 
> 14.000 but when I view it with VMD, it is not any smaller than before.
> 
>  
> 
> Do I have to use other software to achieve this? If so, I’d really 
> appreciate some pointers.
> 

You can do this in three steps.  If your goal is to have a single lipid bilayer 
in the middle of the box, with water around it:

genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919
editconf -f popc_new.pdb -o popc_new2.pdb -c -box 9.6 9.5 14
genbox -cp popc_new2.pdb -cs spc216.gro -o solv.pdb

The reason you need three steps is that if you supply a z-dimension of 14 in the 
first genbox command, at least two full bilayers (or some fraction close to it) 
will be placed in your box.  If that's your goal, then this can be done in one step.

-Justin
>  
> 
> Thanks!
> 
> <<
> 
> Email has been scanned for viruses by UNMC email management service 
> <http://www.nottingham.edu.my>
> 
>  >>
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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