[gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)

[Justin A. Lemkul]

Shay Amram wrote:
> Dear GROMACS users,
> 
>  
> 
> I have been trying to expand a membrane by a non-integer multiplier (for 
> example X1.5). This can be done using
> 
>  
> 
> *genbox -cs Membrane.gro -o Expanded_membrane.gro –box 1.5X 1.5Y Z***
> 
>  
> 
> This has worked very good with _homogenous_ membranes, and only very 
> short equilibrium times were required to re-equilibrate the membrane 
> (~10-20ns).
> 
> Now I am trying to deal the same way with _heterogeneous_ membrane 
> (POPG/POPE mixture, Mikko Karttunen et. al).
> 
>  
> 
> When trying to invoke the above command to the POPG/POPE membrane I get 
> a membrane with different compositions of lipids in the upper and lower 
> leaflets.
> 
> This happens (so I suspect) because the arrangement of lipids in each 
> leaflet is somewhat different so that the molecules that "get' to be 
> multiplied do not conserve the
> 
> same ratio of different lipids as in the original structure (which has 
> ratio of 1:3 POPG/POPE).
> 
>  

If you have an excess of POPE, you can (either manually, or by using a script) 
randomly choose some POPE to be converted to (or replaced with) POPG by some 
clever means.  This is not a trivial task.

> 
> Is there a way to multiply the membrane by a _non-integer_ number AND 
> somehow conserve the ratio of different lipid species too?
> 

The output is dependent upon the configuration of the input and the box size, so 
no, there is no straightforward, automatic, way of doing so given the 
constraints of your box dimensions.

> Or at the very least, to have both upper and lower leaflets identical 
> after multiplication? (This, too, would help immensely).
> 
>  

If you can construct a satisfactory monolayer, you can manipulate its 
coordinates (i.e. horizontal flip and translation) to create a bilayer.  You 
would have to do plenty of equilibration after doing so, of course.

-Justin

> 
> Thanks,
> 
> -Shay
> 
>  
> 
>  
> 
> 
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> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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