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

Shay Amram shayamra at post.tau.ac.il
Wed Jun 3 21:15:25 CEST 2009

Hi Nicolas, 


I'll try that too since I am somewhat familiar with VMD scripting to I may
equilibrate a 2X 2Y 1Z membrane like you specified, 

and have a script find a timeframe where lipid composition fits what I need.






-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Nicolas Sapay
Sent: Wednesday, June 03, 2009 15:23 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)




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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