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

[Shay Amram]

By some fluke one of the layers consists of the lipid ratio I require (while
the other does not).

I will try your suggestion regarding to horizontal flip of that layer.

Thanks!

-Shay

 

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: Tuesday, June 02, 2009 23:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)

 

 

 

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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-- 

========================================

 

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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