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

Nicolas Sapay nicolas.sapay at cermav.cnrs.fr
Wed Jun 3 15:23:20 CEST 2009

Shay Amram a écrit :
> 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).
> Is there a way to multiply the membrane by a _non-integer_ number AND 
> somehow conserve the ratio of different lipid species too?
> Or at the very least, to have both upper and lower leaflets identical 
> after multiplication? (This, too, would help immensely).
This is quite a difficult task unfortunately. Personally, I create a 
membrane patch larger than the one I want (e.g. 2x 2y 1z), load the gro 
file into VMD, then cut a patch the size/composition I need. That means 
doing selections like:

    set sel [atomselect top "same resid as (x<... and x>... and y<...
    and y>...)"]

Checking the number of lipids in each layer:

    [atomselect top "resname DOPG and name P1 and z>... and (same resid
    as (x<... and x>... and y<... and y>...))"] num
    [atomselect top "resname DOPG and name P1 and z<... and (same resid
    as (x<... and x>... and y<... and y>...))"] num

Completing the selection by manually adding the residues I need:

    set sel [atomselect top "same resid as (x<... and x>... and y<...
    and y>...) or resid ..."]

Saving the coordinates:

    animate write pdb sel $sel

This is a tidy task and some equilibration is still required after that. 
Basic knowledge of TCL/VMD scripting languages may be required to 
facilitate/automate the work.

> Thanks,
> -Shay
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