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.
Nicolas
Thanks,
-Shay
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