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

[NG HUI WEN]

Thanks for that guys! I will try them out.

Just a quick question here with regards to my lipids being possibly too
small,  does it have something to do with the minimum image criterion
for PBC? I have ensured that the distance of edge of the box and the
atoms at the side of the protein to be greater than the cutoff of 1.2nm
(PME is used)... in the hope that the protein would not interact with
it's neighbouring image. I hope I'm not going down the wrong direction
in my understanding of pbc...

Thanks!!!

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of
chris.neale at utoronto.ca
Sent: Monday, September 27, 2010 8:30 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] How to make a lipid bilayer with specific
dimensions?

I don't think that this is currently causing anybody any problems, but  
note that genbox is going to cut any lipids that cross out of the  
central unit box (either because genbox is unaware of PBC or because  
these lipids now clash across PBC).

Therefore:

genbox -cs popc128a.pdb -o popc_new.pdb -box 9.6 9.5 6.919

will give you a bilayer that gets solvated with a water defect around  
the edges of the initial unit cell and that, after 10 - 200 ns of  
simulation, gives you an equilibrated bilayer (without water defect)  
that is much smaller than x=9.6, y=9.5.

To get what you want, you need to either start your bilayer with  
larger x and y (calculate area per lipid in 9.6*9.5 to figure out how  
many lipids you should have and keep running genbox until you get  
that), or perhaps a run through inflategro might do it.

Chris.
  --original message --

[gmx-users] How to make a lipid bilayer with specific dimensions?
Justin A. Lemkul jalemkul at vt.edu
Mon Sep 27 13:00:32 CEST 2010

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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>
>
>  >>
>

-- 
========================================

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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